The following packages will be installed:
 pysam 
Fetching README...  0%100%100%100%100%100%Done
Fetching pysam.SlackBuild...  0%100%100%100%100%100%Done
Fetching pysam.info...  0%100%100%100%100%100%Done
Fetching slack-desc...  0%100%100%100%100%100%Done
pysam-0.19.0/
pysam-0.19.0/AUTHORS
pysam-0.19.0/COPYING
pysam-0.19.0/INSTALL
pysam-0.19.0/MANIFEST.in
pysam-0.19.0/NEWS
pysam-0.19.0/PKG-INFO
pysam-0.19.0/README.rst
pysam-0.19.0/bcftools/
pysam-0.19.0/bcftools/HMM.c
pysam-0.19.0/bcftools/HMM.c.pysam.c
pysam-0.19.0/bcftools/HMM.h
pysam-0.19.0/bcftools/LICENSE
pysam-0.19.0/bcftools/README
pysam-0.19.0/bcftools/abuf.c
pysam-0.19.0/bcftools/abuf.c.pysam.c
pysam-0.19.0/bcftools/abuf.h
pysam-0.19.0/bcftools/bam2bcf.c
pysam-0.19.0/bcftools/bam2bcf.c.pysam.c
pysam-0.19.0/bcftools/bam2bcf.h
pysam-0.19.0/bcftools/bam2bcf_indel.c
pysam-0.19.0/bcftools/bam2bcf_indel.c.pysam.c
pysam-0.19.0/bcftools/bam_sample.c
pysam-0.19.0/bcftools/bam_sample.c.pysam.c
pysam-0.19.0/bcftools/bam_sample.h
pysam-0.19.0/bcftools/bcftools.h
pysam-0.19.0/bcftools/bcftools.pysam.c
pysam-0.19.0/bcftools/bcftools.pysam.h
pysam-0.19.0/bcftools/bin.c
pysam-0.19.0/bcftools/bin.c.pysam.c
pysam-0.19.0/bcftools/bin.h
pysam-0.19.0/bcftools/call.h
pysam-0.19.0/bcftools/ccall.c
pysam-0.19.0/bcftools/ccall.c.pysam.c
pysam-0.19.0/bcftools/cols.c
pysam-0.19.0/bcftools/cols.c.pysam.c
pysam-0.19.0/bcftools/cols.h
pysam-0.19.0/bcftools/consensus.c
pysam-0.19.0/bcftools/consensus.c.pysam.c
pysam-0.19.0/bcftools/convert.c
pysam-0.19.0/bcftools/convert.c.pysam.c
pysam-0.19.0/bcftools/convert.h
pysam-0.19.0/bcftools/csq.c
pysam-0.19.0/bcftools/csq.c.pysam.c
pysam-0.19.0/bcftools/dist.c
pysam-0.19.0/bcftools/dist.c.pysam.c
pysam-0.19.0/bcftools/dist.h
pysam-0.19.0/bcftools/em.c
pysam-0.19.0/bcftools/em.c.pysam.c
pysam-0.19.0/bcftools/extsort.c
pysam-0.19.0/bcftools/extsort.c.pysam.c
pysam-0.19.0/bcftools/extsort.h
pysam-0.19.0/bcftools/filter.c
pysam-0.19.0/bcftools/filter.c.pysam.c
pysam-0.19.0/bcftools/filter.h
pysam-0.19.0/bcftools/gvcf.c
pysam-0.19.0/bcftools/gvcf.c.pysam.c
pysam-0.19.0/bcftools/gvcf.h
pysam-0.19.0/bcftools/hclust.c
pysam-0.19.0/bcftools/hclust.c.pysam.c
pysam-0.19.0/bcftools/hclust.h
pysam-0.19.0/bcftools/hex.h
pysam-0.19.0/bcftools/khash_str2str.h
pysam-0.19.0/bcftools/kheap.h
pysam-0.19.0/bcftools/kmin.c
pysam-0.19.0/bcftools/kmin.c.pysam.c
pysam-0.19.0/bcftools/kmin.h
pysam-0.19.0/bcftools/main.c
pysam-0.19.0/bcftools/main.c.pysam.c
pysam-0.19.0/bcftools/mcall.c
pysam-0.19.0/bcftools/mcall.c.pysam.c
pysam-0.19.0/bcftools/mpileup.c
pysam-0.19.0/bcftools/mpileup.c.pysam.c
pysam-0.19.0/bcftools/mw.h
pysam-0.19.0/bcftools/ploidy.c
pysam-0.19.0/bcftools/ploidy.c.pysam.c
pysam-0.19.0/bcftools/ploidy.h
pysam-0.19.0/bcftools/prob1.c
pysam-0.19.0/bcftools/prob1.c.pysam.c
pysam-0.19.0/bcftools/prob1.h
pysam-0.19.0/bcftools/rbuf.h
pysam-0.19.0/bcftools/regidx.c
pysam-0.19.0/bcftools/regidx.c.pysam.c
pysam-0.19.0/bcftools/regidx.h
pysam-0.19.0/bcftools/reheader.c
pysam-0.19.0/bcftools/reheader.c.pysam.c
pysam-0.19.0/bcftools/smpl_ilist.c
pysam-0.19.0/bcftools/smpl_ilist.c.pysam.c
pysam-0.19.0/bcftools/smpl_ilist.h
pysam-0.19.0/bcftools/str_finder.c
pysam-0.19.0/bcftools/str_finder.c.pysam.c
pysam-0.19.0/bcftools/str_finder.h
pysam-0.19.0/bcftools/tabix.c
pysam-0.19.0/bcftools/tabix.c.pysam.c
pysam-0.19.0/bcftools/tsv2vcf.c
pysam-0.19.0/bcftools/tsv2vcf.c.pysam.c
pysam-0.19.0/bcftools/tsv2vcf.h
pysam-0.19.0/bcftools/utlist.h
pysam-0.19.0/bcftools/variantkey.h
pysam-0.19.0/bcftools/vcfannotate.c
pysam-0.19.0/bcftools/vcfannotate.c.pysam.c
pysam-0.19.0/bcftools/vcfbuf.c
pysam-0.19.0/bcftools/vcfbuf.c.pysam.c
pysam-0.19.0/bcftools/vcfbuf.h
pysam-0.19.0/bcftools/vcfcall.c
pysam-0.19.0/bcftools/vcfcall.c.pysam.c
pysam-0.19.0/bcftools/vcfcnv.c
pysam-0.19.0/bcftools/vcfcnv.c.pysam.c
pysam-0.19.0/bcftools/vcfconcat.c
pysam-0.19.0/bcftools/vcfconcat.c.pysam.c
pysam-0.19.0/bcftools/vcfconvert.c
pysam-0.19.0/bcftools/vcfconvert.c.pysam.c
pysam-0.19.0/bcftools/vcffilter.c
pysam-0.19.0/bcftools/vcffilter.c.pysam.c
pysam-0.19.0/bcftools/vcfgtcheck.c
pysam-0.19.0/bcftools/vcfgtcheck.c.pysam.c
pysam-0.19.0/bcftools/vcfhead.c
pysam-0.19.0/bcftools/vcfhead.c.pysam.c
pysam-0.19.0/bcftools/vcfindex.c
pysam-0.19.0/bcftools/vcfindex.c.pysam.c
pysam-0.19.0/bcftools/vcfisec.c
pysam-0.19.0/bcftools/vcfisec.c.pysam.c
pysam-0.19.0/bcftools/vcfmerge.c
pysam-0.19.0/bcftools/vcfmerge.c.pysam.c
pysam-0.19.0/bcftools/vcfnorm.c
pysam-0.19.0/bcftools/vcfnorm.c.pysam.c
pysam-0.19.0/bcftools/vcfplugin.c
pysam-0.19.0/bcftools/vcfplugin.c.pysam.c
pysam-0.19.0/bcftools/vcfquery.c
pysam-0.19.0/bcftools/vcfquery.c.pysam.c
pysam-0.19.0/bcftools/vcfroh.c
pysam-0.19.0/bcftools/vcfroh.c.pysam.c
pysam-0.19.0/bcftools/vcfsom.c
pysam-0.19.0/bcftools/vcfsom.c.pysam.c
pysam-0.19.0/bcftools/vcfsort.c
pysam-0.19.0/bcftools/vcfsort.c.pysam.c
pysam-0.19.0/bcftools/vcfstats.c
pysam-0.19.0/bcftools/vcfstats.c.pysam.c
pysam-0.19.0/bcftools/vcfview.c
pysam-0.19.0/bcftools/vcfview.c.pysam.c
pysam-0.19.0/bcftools/vcmp.c
pysam-0.19.0/bcftools/vcmp.c.pysam.c
pysam-0.19.0/bcftools/vcmp.h
pysam-0.19.0/bcftools/version.c
pysam-0.19.0/bcftools/version.c.pysam.c
pysam-0.19.0/bcftools/version.sh
pysam-0.19.0/cy_build.py
pysam-0.19.0/doc/
pysam-0.19.0/doc/Makefile
pysam-0.19.0/doc/api.rst
pysam-0.19.0/doc/benchmarking.rst
pysam-0.19.0/doc/conf.py
pysam-0.19.0/doc/developer.rst
pysam-0.19.0/doc/faq.rst
pysam-0.19.0/doc/glossary.rst
pysam-0.19.0/doc/index.rst
pysam-0.19.0/doc/installation.rst
pysam-0.19.0/doc/make.bat
pysam-0.19.0/doc/release.rst
pysam-0.19.0/doc/usage.rst
pysam-0.19.0/htslib/
pysam-0.19.0/htslib/LICENSE
pysam-0.19.0/htslib/Makefile
pysam-0.19.0/htslib/README
pysam-0.19.0/htslib/bcf_sr_sort.c
pysam-0.19.0/htslib/bcf_sr_sort.h
pysam-0.19.0/htslib/bgzf.c
pysam-0.19.0/htslib/bgzip.c
pysam-0.19.0/htslib/builddir_vars.mk.in
pysam-0.19.0/htslib/config.h.in
pysam-0.19.0/htslib/config.mk.in
pysam-0.19.0/htslib/configure
pysam-0.19.0/htslib/configure.ac
pysam-0.19.0/htslib/cram/
pysam-0.19.0/htslib/cram/cram.h
pysam-0.19.0/htslib/cram/cram_codecs.c
pysam-0.19.0/htslib/cram/cram_codecs.h
pysam-0.19.0/htslib/cram/cram_decode.c
pysam-0.19.0/htslib/cram/cram_decode.h
pysam-0.19.0/htslib/cram/cram_encode.c
pysam-0.19.0/htslib/cram/cram_encode.h
pysam-0.19.0/htslib/cram/cram_external.c
pysam-0.19.0/htslib/cram/cram_index.c
pysam-0.19.0/htslib/cram/cram_index.h
pysam-0.19.0/htslib/cram/cram_io.c
pysam-0.19.0/htslib/cram/cram_io.h
pysam-0.19.0/htslib/cram/cram_samtools.h
pysam-0.19.0/htslib/cram/cram_stats.c
pysam-0.19.0/htslib/cram/cram_stats.h
pysam-0.19.0/htslib/cram/cram_structs.h
pysam-0.19.0/htslib/cram/mFILE.c
pysam-0.19.0/htslib/cram/mFILE.h
pysam-0.19.0/htslib/cram/misc.h
pysam-0.19.0/htslib/cram/open_trace_file.c
pysam-0.19.0/htslib/cram/open_trace_file.h
pysam-0.19.0/htslib/cram/os.h
pysam-0.19.0/htslib/cram/pooled_alloc.c
pysam-0.19.0/htslib/cram/pooled_alloc.h
pysam-0.19.0/htslib/cram/string_alloc.c
pysam-0.19.0/htslib/cram/string_alloc.h
pysam-0.19.0/htslib/errmod.c
pysam-0.19.0/htslib/faidx.c
pysam-0.19.0/htslib/header.c
pysam-0.19.0/htslib/header.h
pysam-0.19.0/htslib/hfile.c
pysam-0.19.0/htslib/hfile_gcs.c
pysam-0.19.0/htslib/hfile_internal.h
pysam-0.19.0/htslib/hfile_libcurl.c
pysam-0.19.0/htslib/hfile_s3.c
pysam-0.19.0/htslib/hfile_s3_write.c
pysam-0.19.0/htslib/hts.c
pysam-0.19.0/htslib/hts_expr.c
pysam-0.19.0/htslib/hts_internal.h
pysam-0.19.0/htslib/hts_os.c
pysam-0.19.0/htslib/htscodecs/
pysam-0.19.0/htslib/htscodecs/htscodecs/
pysam-0.19.0/htslib/htscodecs/htscodecs/arith_dynamic.c
pysam-0.19.0/htslib/htscodecs/htscodecs/arith_dynamic.h
pysam-0.19.0/htslib/htscodecs/htscodecs/c_range_coder.h
pysam-0.19.0/htslib/htscodecs/htscodecs/c_simple_model.h
pysam-0.19.0/htslib/htscodecs/htscodecs/fqzcomp_qual.c
pysam-0.19.0/htslib/htscodecs/htscodecs/fqzcomp_qual.h
pysam-0.19.0/htslib/htscodecs/htscodecs/htscodecs.c
pysam-0.19.0/htslib/htscodecs/htscodecs/htscodecs.h
pysam-0.19.0/htslib/htscodecs/htscodecs/htscodecs_endian.h
pysam-0.19.0/htslib/htscodecs/htscodecs/pack.c
pysam-0.19.0/htslib/htscodecs/htscodecs/pack.h
pysam-0.19.0/htslib/htscodecs/htscodecs/pooled_alloc.h
pysam-0.19.0/htslib/htscodecs/htscodecs/rANS_byte.h
pysam-0.19.0/htslib/htscodecs/htscodecs/rANS_static.c
pysam-0.19.0/htslib/htscodecs/htscodecs/rANS_static.h
pysam-0.19.0/htslib/htscodecs/htscodecs/rANS_static4x16.h
pysam-0.19.0/htslib/htscodecs/htscodecs/rANS_static4x16pr.c
pysam-0.19.0/htslib/htscodecs/htscodecs/rANS_word.h
pysam-0.19.0/htslib/htscodecs/htscodecs/rle.c
pysam-0.19.0/htslib/htscodecs/htscodecs/rle.h
pysam-0.19.0/htslib/htscodecs/htscodecs/tokenise_name3.c
pysam-0.19.0/htslib/htscodecs/htscodecs/tokenise_name3.h
pysam-0.19.0/htslib/htscodecs/htscodecs/utils.h
pysam-0.19.0/htslib/htscodecs/htscodecs/varint.h
pysam-0.19.0/htslib/htscodecs/htscodecs/varint2.h
pysam-0.19.0/htslib/htscodecs/htscodecs/version.h
pysam-0.19.0/htslib/htscodecs_bundled.mk
pysam-0.19.0/htslib/htscodecs_external.mk
pysam-0.19.0/htslib/htsfile.c
pysam-0.19.0/htslib/htslib/
pysam-0.19.0/htslib/htslib/bgzf.h
pysam-0.19.0/htslib/htslib/cram.h
pysam-0.19.0/htslib/htslib/faidx.h
pysam-0.19.0/htslib/htslib/hfile.h
pysam-0.19.0/htslib/htslib/hts.h
pysam-0.19.0/htslib/htslib/hts_defs.h
pysam-0.19.0/htslib/htslib/hts_endian.h
pysam-0.19.0/htslib/htslib/hts_expr.h
pysam-0.19.0/htslib/htslib/hts_log.h
pysam-0.19.0/htslib/htslib/hts_os.h
pysam-0.19.0/htslib/htslib/kbitset.h
pysam-0.19.0/htslib/htslib/kfunc.h
pysam-0.19.0/htslib/htslib/khash.h
pysam-0.19.0/htslib/htslib/khash_str2int.h
pysam-0.19.0/htslib/htslib/klist.h
pysam-0.19.0/htslib/htslib/knetfile.h
pysam-0.19.0/htslib/htslib/kroundup.h
pysam-0.19.0/htslib/htslib/kseq.h
pysam-0.19.0/htslib/htslib/ksort.h
pysam-0.19.0/htslib/htslib/kstring.h
pysam-0.19.0/htslib/htslib/regidx.h
pysam-0.19.0/htslib/htslib/sam.h
pysam-0.19.0/htslib/htslib/synced_bcf_reader.h
pysam-0.19.0/htslib/htslib/tbx.h
pysam-0.19.0/htslib/htslib/thread_pool.h
pysam-0.19.0/htslib/htslib/vcf.h
pysam-0.19.0/htslib/htslib/vcf_sweep.h
pysam-0.19.0/htslib/htslib/vcfutils.h
pysam-0.19.0/htslib/htslib.mk
pysam-0.19.0/htslib/htslib.pc.in
pysam-0.19.0/htslib/htslib_vars.mk
pysam-0.19.0/htslib/kfunc.c
pysam-0.19.0/htslib/kstring.c
pysam-0.19.0/htslib/m4/
pysam-0.19.0/htslib/m4/hts_hide_dynamic_syms.m4
pysam-0.19.0/htslib/m4/hts_prog_cc_warnings.m4
pysam-0.19.0/htslib/m4/pkg.m4
pysam-0.19.0/htslib/md5.c
pysam-0.19.0/htslib/multipart.c
pysam-0.19.0/htslib/os/
pysam-0.19.0/htslib/os/lzma_stub.h
pysam-0.19.0/htslib/os/rand.c
pysam-0.19.0/htslib/plugin.c
pysam-0.19.0/htslib/probaln.c
pysam-0.19.0/htslib/realn.c
pysam-0.19.0/htslib/regidx.c
pysam-0.19.0/htslib/region.c
pysam-0.19.0/htslib/sam.c
pysam-0.19.0/htslib/sam_internal.h
pysam-0.19.0/htslib/synced_bcf_reader.c
pysam-0.19.0/htslib/tabix.c
pysam-0.19.0/htslib/tbx.c
pysam-0.19.0/htslib/textutils.c
pysam-0.19.0/htslib/textutils_internal.h
pysam-0.19.0/htslib/thread_pool.c
pysam-0.19.0/htslib/thread_pool_internal.h
pysam-0.19.0/htslib/vcf.c
pysam-0.19.0/htslib/vcf_sweep.c
pysam-0.19.0/htslib/vcfutils.c
pysam-0.19.0/htslib/version.sh
pysam-0.19.0/pysam/
pysam-0.19.0/pysam/Pileup.py
pysam-0.19.0/pysam/__init__.py
pysam-0.19.0/pysam/bcftools.py
pysam-0.19.0/pysam/cbcftools_util.h
pysam-0.19.0/pysam/csamtools_util.h
pysam-0.19.0/pysam/htslib_util.c
pysam-0.19.0/pysam/htslib_util.h
pysam-0.19.0/pysam/include/
pysam-0.19.0/pysam/include/__init__.py
pysam-0.19.0/pysam/libcalignedsegment.c
pysam-0.19.0/pysam/libcalignedsegment.pxd
pysam-0.19.0/pysam/libcalignedsegment.pyi
pysam-0.19.0/pysam/libcalignedsegment.pyx
pysam-0.19.0/pysam/libcalignmentfile.c
pysam-0.19.0/pysam/libcalignmentfile.pxd
pysam-0.19.0/pysam/libcalignmentfile.pyi
pysam-0.19.0/pysam/libcalignmentfile.pyx
pysam-0.19.0/pysam/libcbcf.c
pysam-0.19.0/pysam/libcbcf.pxd
pysam-0.19.0/pysam/libcbcf.pyi
pysam-0.19.0/pysam/libcbcf.pyx
pysam-0.19.0/pysam/libcbcftools.c
pysam-0.19.0/pysam/libcbcftools.pxd
pysam-0.19.0/pysam/libcbcftools.pyi
pysam-0.19.0/pysam/libcbcftools.pyx
pysam-0.19.0/pysam/libcbgzf.c
pysam-0.19.0/pysam/libcbgzf.pyi
pysam-0.19.0/pysam/libcbgzf.pyx
pysam-0.19.0/pysam/libcfaidx.c
pysam-0.19.0/pysam/libcfaidx.pxd
pysam-0.19.0/pysam/libcfaidx.pyi
pysam-0.19.0/pysam/libcfaidx.pyx
pysam-0.19.0/pysam/libchtslib.c
pysam-0.19.0/pysam/libchtslib.pxd
pysam-0.19.0/pysam/libchtslib.pyi
pysam-0.19.0/pysam/libchtslib.pyx
pysam-0.19.0/pysam/libcsamfile.c
pysam-0.19.0/pysam/libcsamfile.pxd
pysam-0.19.0/pysam/libcsamfile.pyi
pysam-0.19.0/pysam/libcsamfile.pyx
pysam-0.19.0/pysam/libcsamtools.c
pysam-0.19.0/pysam/libcsamtools.pxd
pysam-0.19.0/pysam/libcsamtools.pyi
pysam-0.19.0/pysam/libcsamtools.pyx
pysam-0.19.0/pysam/libctabix.c
pysam-0.19.0/pysam/libctabix.pxd
pysam-0.19.0/pysam/libctabix.pyi
pysam-0.19.0/pysam/libctabix.pyx
pysam-0.19.0/pysam/libctabixproxies.c
pysam-0.19.0/pysam/libctabixproxies.pxd
pysam-0.19.0/pysam/libctabixproxies.pyi
pysam-0.19.0/pysam/libctabixproxies.pyx
pysam-0.19.0/pysam/libcutils.c
pysam-0.19.0/pysam/libcutils.pxd
pysam-0.19.0/pysam/libcutils.pyi
pysam-0.19.0/pysam/libcutils.pyx
pysam-0.19.0/pysam/libcvcf.c
pysam-0.19.0/pysam/libcvcf.pxd
pysam-0.19.0/pysam/libcvcf.pyi
pysam-0.19.0/pysam/libcvcf.pyx
pysam-0.19.0/pysam/py.typed
pysam-0.19.0/pysam/pysam_stream.h
pysam-0.19.0/pysam/pysam_util.c
pysam-0.19.0/pysam/pysam_util.h
pysam-0.19.0/pysam/samtools.py
pysam-0.19.0/pysam/utils.py
pysam-0.19.0/pysam/version.h
pysam-0.19.0/pysam/version.py
pysam-0.19.0/pysam/version.pyi
pysam-0.19.0/pysam.egg-info/
pysam-0.19.0/pysam.egg-info/PKG-INFO
pysam-0.19.0/pysam.egg-info/SOURCES.txt
pysam-0.19.0/pysam.egg-info/dependency_links.txt
pysam-0.19.0/pysam.egg-info/not-zip-safe
pysam-0.19.0/pysam.egg-info/top_level.txt
pysam-0.19.0/requirements.txt
pysam-0.19.0/samtools/
pysam-0.19.0/samtools/LICENSE
pysam-0.19.0/samtools/README
pysam-0.19.0/samtools/amplicon_stats.c
pysam-0.19.0/samtools/amplicon_stats.c.pysam.c
pysam-0.19.0/samtools/bam.c
pysam-0.19.0/samtools/bam.c.pysam.c
pysam-0.19.0/samtools/bam.h
pysam-0.19.0/samtools/bam2depth.c
pysam-0.19.0/samtools/bam2depth.c.pysam.c
pysam-0.19.0/samtools/bam_addrprg.c
pysam-0.19.0/samtools/bam_addrprg.c.pysam.c
pysam-0.19.0/samtools/bam_ampliconclip.c
pysam-0.19.0/samtools/bam_ampliconclip.c.pysam.c
pysam-0.19.0/samtools/bam_ampliconclip.h
pysam-0.19.0/samtools/bam_aux.c
pysam-0.19.0/samtools/bam_aux.c.pysam.c
pysam-0.19.0/samtools/bam_cat.c
pysam-0.19.0/samtools/bam_cat.c.pysam.c
pysam-0.19.0/samtools/bam_color.c
pysam-0.19.0/samtools/bam_color.c.pysam.c
pysam-0.19.0/samtools/bam_consensus.c
pysam-0.19.0/samtools/bam_consensus.c.pysam.c
pysam-0.19.0/samtools/bam_fastq.c
pysam-0.19.0/samtools/bam_fastq.c.pysam.c
pysam-0.19.0/samtools/bam_flags.c
pysam-0.19.0/samtools/bam_flags.c.pysam.c
pysam-0.19.0/samtools/bam_import.c
pysam-0.19.0/samtools/bam_import.c.pysam.c
pysam-0.19.0/samtools/bam_index.c
pysam-0.19.0/samtools/bam_index.c.pysam.c
pysam-0.19.0/samtools/bam_lpileup.c
pysam-0.19.0/samtools/bam_lpileup.c.pysam.c
pysam-0.19.0/samtools/bam_lpileup.h
pysam-0.19.0/samtools/bam_markdup.c
pysam-0.19.0/samtools/bam_markdup.c.pysam.c
pysam-0.19.0/samtools/bam_mate.c
pysam-0.19.0/samtools/bam_mate.c.pysam.c
pysam-0.19.0/samtools/bam_md.c
pysam-0.19.0/samtools/bam_md.c.pysam.c
pysam-0.19.0/samtools/bam_plbuf.c
pysam-0.19.0/samtools/bam_plbuf.c.pysam.c
pysam-0.19.0/samtools/bam_plbuf.h
pysam-0.19.0/samtools/bam_plcmd.c
pysam-0.19.0/samtools/bam_plcmd.c.pysam.c
pysam-0.19.0/samtools/bam_quickcheck.c
pysam-0.19.0/samtools/bam_quickcheck.c.pysam.c
pysam-0.19.0/samtools/bam_reheader.c
pysam-0.19.0/samtools/bam_reheader.c.pysam.c
pysam-0.19.0/samtools/bam_rmdup.c
pysam-0.19.0/samtools/bam_rmdup.c.pysam.c
pysam-0.19.0/samtools/bam_rmdupse.c
pysam-0.19.0/samtools/bam_rmdupse.c.pysam.c
pysam-0.19.0/samtools/bam_samples.c
pysam-0.19.0/samtools/bam_samples.c.pysam.c
pysam-0.19.0/samtools/bam_sort.c
pysam-0.19.0/samtools/bam_sort.c.pysam.c
pysam-0.19.0/samtools/bam_split.c
pysam-0.19.0/samtools/bam_split.c.pysam.c
pysam-0.19.0/samtools/bam_stat.c
pysam-0.19.0/samtools/bam_stat.c.pysam.c
pysam-0.19.0/samtools/bamshuf.c
pysam-0.19.0/samtools/bamshuf.c.pysam.c
pysam-0.19.0/samtools/bamtk.c
pysam-0.19.0/samtools/bamtk.c.pysam.c
pysam-0.19.0/samtools/bedcov.c
pysam-0.19.0/samtools/bedcov.c.pysam.c
pysam-0.19.0/samtools/bedidx.c
pysam-0.19.0/samtools/bedidx.c.pysam.c
pysam-0.19.0/samtools/bedidx.h
pysam-0.19.0/samtools/consensus_pileup.c
pysam-0.19.0/samtools/consensus_pileup.c.pysam.c
pysam-0.19.0/samtools/consensus_pileup.h
pysam-0.19.0/samtools/coverage.c
pysam-0.19.0/samtools/coverage.c.pysam.c
pysam-0.19.0/samtools/cut_target.c
pysam-0.19.0/samtools/cut_target.c.pysam.c
pysam-0.19.0/samtools/dict.c
pysam-0.19.0/samtools/dict.c.pysam.c
pysam-0.19.0/samtools/faidx.c
pysam-0.19.0/samtools/faidx.c.pysam.c
pysam-0.19.0/samtools/lz4/
pysam-0.19.0/samtools/lz4/LICENSE
pysam-0.19.0/samtools/lz4/lz4.c
pysam-0.19.0/samtools/lz4/lz4.c.pysam.c
pysam-0.19.0/samtools/lz4/lz4.h
pysam-0.19.0/samtools/padding.c
pysam-0.19.0/samtools/padding.c.pysam.c
pysam-0.19.0/samtools/phase.c
pysam-0.19.0/samtools/phase.c.pysam.c
pysam-0.19.0/samtools/sam_opts.c
pysam-0.19.0/samtools/sam_opts.c.pysam.c
pysam-0.19.0/samtools/sam_opts.h
pysam-0.19.0/samtools/sam_utils.c
pysam-0.19.0/samtools/sam_utils.c.pysam.c
pysam-0.19.0/samtools/sam_view.c
pysam-0.19.0/samtools/sam_view.c.pysam.c
pysam-0.19.0/samtools/sample.c
pysam-0.19.0/samtools/sample.c.pysam.c
pysam-0.19.0/samtools/sample.h
pysam-0.19.0/samtools/samtools.h
pysam-0.19.0/samtools/samtools.pysam.c
pysam-0.19.0/samtools/samtools.pysam.h
pysam-0.19.0/samtools/splaysort.h
pysam-0.19.0/samtools/stats.c
pysam-0.19.0/samtools/stats.c.pysam.c
pysam-0.19.0/samtools/stats_isize.c
pysam-0.19.0/samtools/stats_isize.c.pysam.c
pysam-0.19.0/samtools/stats_isize.h
pysam-0.19.0/samtools/tmp_file.c
pysam-0.19.0/samtools/tmp_file.c.pysam.c
pysam-0.19.0/samtools/tmp_file.h
pysam-0.19.0/samtools/version.sh
pysam-0.19.0/setup.cfg
pysam-0.19.0/setup.py
pysam-0.19.0/win32/
pysam-0.19.0/win32/getopt.c
pysam-0.19.0/win32/getopt.h
pysam-0.19.0/win32/stdint.h
pysam-0.19.0/win32/unistd.h
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: (sysconfig) CC=gcc -pthread
# pysam: (sysconfig) CFLAGS=-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
# pysam: (sysconfig) LDFLAGS=
checking for gcc... gcc -pthread
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -pthread accepts -g... yes
checking for gcc -pthread option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... unknown
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking shared library type for unknown-Linux... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... gcc -pthread -E
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking for srand48_deterministic... no
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking whether htscodecs files are present... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking for curl/curl.h... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... no
checking for library containing HMAC... -lcrypto
checking for library containing regcomp... none required
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: linking htscodecs_bundled.mk to htscodecs.mk
# pysam: htslib configure options: --enable-libcurl
# pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o hfile_gcs.o hfile_s3.o hfile_s3_write.o
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm -lcurl -lcrypto
# pysam: htslib_config PLATFORM=default
# pysam: config_option: ENABLE_GCS=1
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: ENABLE_S3=1
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_HMAC=1
# pysam: config_option: HAVE_LIBBZ2=1
# pysam: config_option: HAVE_LIBCURL=1
# pysam: config_option: HAVE_LIBDEFLATE=0
# pysam: config_option: HAVE_LIBLZMA=1
# pysam: config_option: HAVE_MMAP=1
running install
running build
running build_py
creating build
creating build/lib.linux-i686-3.9
creating build/lib.linux-i686-3.9/pysam
copying pysam/Pileup.py -> build/lib.linux-i686-3.9/pysam
copying pysam/__init__.py -> build/lib.linux-i686-3.9/pysam
copying pysam/bcftools.py -> build/lib.linux-i686-3.9/pysam
copying pysam/samtools.py -> build/lib.linux-i686-3.9/pysam
copying pysam/utils.py -> build/lib.linux-i686-3.9/pysam
copying pysam/version.py -> build/lib.linux-i686-3.9/pysam
copying pysam/config.py -> build/lib.linux-i686-3.9/pysam
creating build/lib.linux-i686-3.9/pysam/include
copying pysam/include/__init__.py -> build/lib.linux-i686-3.9/pysam/include
copying pysam/libcalignedsegment.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libcbcf.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libcbcftools.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libcfaidx.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libchtslib.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libcsamfile.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libcsamtools.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libctabix.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libctabixproxies.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libcutils.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/libcvcf.pxd -> build/lib.linux-i686-3.9/pysam
copying pysam/cbcftools_util.h -> build/lib.linux-i686-3.9/pysam
copying pysam/csamtools_util.h -> build/lib.linux-i686-3.9/pysam
copying pysam/htslib_util.h -> build/lib.linux-i686-3.9/pysam
copying pysam/pysam_stream.h -> build/lib.linux-i686-3.9/pysam
copying pysam/pysam_util.h -> build/lib.linux-i686-3.9/pysam
copying pysam/version.h -> build/lib.linux-i686-3.9/pysam
copying pysam/py.typed -> build/lib.linux-i686-3.9/pysam
copying pysam/libcalignedsegment.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libcalignmentfile.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libcbcf.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libcbcftools.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libcbgzf.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libcfaidx.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libchtslib.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libcsamfile.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libcsamtools.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libctabix.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libctabixproxies.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libcutils.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/libcvcf.pyi -> build/lib.linux-i686-3.9/pysam
copying pysam/version.pyi -> build/lib.linux-i686-3.9/pysam
creating build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/bam.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/bam_ampliconclip.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/bedidx.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/consensus_pileup.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/sample.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/samtools.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/samtools.pysam.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/splaysort.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/tmp_file.h -> build/lib.linux-i686-3.9/pysam/include/samtools
copying samtools/config.h -> build/lib.linux-i686-3.9/pysam/include/samtools
creating build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/abuf.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/bam2bcf.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/bin.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/call.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/cols.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/convert.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/dist.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/extsort.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/gvcf.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/hex.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/kheap.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/ploidy.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/regidx.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/str_finder.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/utlist.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/variantkey.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/vcfbuf.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
copying bcftools/config.h -> build/lib.linux-i686-3.9/pysam/include/bcftools
creating build/lib.linux-i686-3.9/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> build/lib.linux-i686-3.9/pysam/include/htslib
copying htslib/header.h -> build/lib.linux-i686-3.9/pysam/include/htslib
copying htslib/hfile_internal.h -> build/lib.linux-i686-3.9/pysam/include/htslib
copying htslib/hts_internal.h -> build/lib.linux-i686-3.9/pysam/include/htslib
copying htslib/sam_internal.h -> build/lib.linux-i686-3.9/pysam/include/htslib
copying htslib/textutils_internal.h -> build/lib.linux-i686-3.9/pysam/include/htslib
copying htslib/thread_pool_internal.h -> build/lib.linux-i686-3.9/pysam/include/htslib
copying htslib/config.h -> build/lib.linux-i686-3.9/pysam/include/htslib
creating build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/hts_expr.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/hts_os.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/kroundup.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.linux-i686-3.9/pysam/include/htslib/htslib
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
creating htslib/config_vars.h for 'pysam.libchtslib' extension
building 'pysam.libchtslib' extension
creating build/temp.linux-i686-3.9
creating build/temp.linux-i686-3.9/pysam
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/htslib_util.c -o build/temp.linux-i686-3.9/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libchtslib.c -o build/temp.linux-i686-3.9/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/htslib_util.o build/temp.linux-i686-3.9/pysam/libchtslib.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -o build/lib.linux-i686-3.9/pysam/libchtslib.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension
building 'pysam.libcsamtools' extension
creating build/temp.linux-i686-3.9/samtools
creating build/temp.linux-i686-3.9/samtools/lz4
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libcsamtools.c -o build/temp.linux-i686-3.9/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-i686-3.9/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_color.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_import.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_index.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_md.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_split.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bamtk.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bedcov.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/bedidx.c.pysam.c -o build/temp.linux-i686-3.9/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-i686-3.9/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/coverage.c.pysam.c -o build/temp.linux-i686-3.9/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/cut_target.c.pysam.c -o build/temp.linux-i686-3.9/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/dict.c.pysam.c -o build/temp.linux-i686-3.9/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/faidx.c.pysam.c -o build/temp.linux-i686-3.9/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/lz4/lz4.c -o build/temp.linux-i686-3.9/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/padding.c.pysam.c -o build/temp.linux-i686-3.9/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/phase.c.pysam.c -o build/temp.linux-i686-3.9/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-i686-3.9/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-i686-3.9/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/sam_view.c.pysam.c -o build/temp.linux-i686-3.9/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/sample.c.pysam.c -o build/temp.linux-i686-3.9/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/samtools.pysam.c -o build/temp.linux-i686-3.9/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/stats.c.pysam.c -o build/temp.linux-i686-3.9/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-i686-3.9/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-i686-3.9/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libcsamtools.o build/temp.linux-i686-3.9/samtools/amplicon_stats.c.pysam.o build/temp.linux-i686-3.9/samtools/bam.c.pysam.o build/temp.linux-i686-3.9/samtools/bam2depth.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_addrprg.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_aux.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_cat.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_color.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_consensus.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_fastq.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_flags.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_import.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_index.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_lpileup.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_markdup.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_mate.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_md.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_plbuf.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_plcmd.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_quickcheck.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_reheader.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_rmdup.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_rmdupse.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_samples.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_sort.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_split.c.pysam.o build/temp.linux-i686-3.9/samtools/bam_stat.c.pysam.o build/temp.linux-i686-3.9/samtools/bamshuf.c.pysam.o build/temp.linux-i686-3.9/samtools/bamtk.c.pysam.o build/temp.linux-i686-3.9/samtools/bedcov.c.pysam.o build/temp.linux-i686-3.9/samtools/bedidx.c.pysam.o build/temp.linux-i686-3.9/samtools/consensus_pileup.c.pysam.o build/temp.linux-i686-3.9/samtools/coverage.c.pysam.o build/temp.linux-i686-3.9/samtools/cut_target.c.pysam.o build/temp.linux-i686-3.9/samtools/dict.c.pysam.o build/temp.linux-i686-3.9/samtools/faidx.c.pysam.o build/temp.linux-i686-3.9/samtools/lz4/lz4.o build/temp.linux-i686-3.9/samtools/padding.c.pysam.o build/temp.linux-i686-3.9/samtools/phase.c.pysam.o build/temp.linux-i686-3.9/samtools/sam_opts.c.pysam.o build/temp.linux-i686-3.9/samtools/sam_utils.c.pysam.o build/temp.linux-i686-3.9/samtools/sam_view.c.pysam.o build/temp.linux-i686-3.9/samtools/sample.c.pysam.o build/temp.linux-i686-3.9/samtools/samtools.pysam.o build/temp.linux-i686-3.9/samtools/stats.c.pysam.o build/temp.linux-i686-3.9/samtools/stats_isize.c.pysam.o build/temp.linux-i686-3.9/samtools/tmp_file.c.pysam.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libcsamtools.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating build/temp.linux-i686-3.9/bcftools
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/HMM.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/abuf.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/bcftools.pysam.c -o build/temp.linux-i686-3.9/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/bin.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/ccall.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/cols.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/consensus.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/convert.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/csq.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/dist.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/em.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/extsort.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/filter.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/hclust.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/kmin.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/main.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/mcall.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/prob1.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/regidx.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/reheader.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/tabix.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c bcftools/version.c.pysam.c -o build/temp.linux-i686-3.9/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libcbcftools.c -o build/temp.linux-i686-3.9/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/bcftools/HMM.c.pysam.o build/temp.linux-i686-3.9/bcftools/abuf.c.pysam.o build/temp.linux-i686-3.9/bcftools/bam2bcf.c.pysam.o build/temp.linux-i686-3.9/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-i686-3.9/bcftools/bam_sample.c.pysam.o build/temp.linux-i686-3.9/bcftools/bcftools.pysam.o build/temp.linux-i686-3.9/bcftools/bin.c.pysam.o build/temp.linux-i686-3.9/bcftools/ccall.c.pysam.o build/temp.linux-i686-3.9/bcftools/cols.c.pysam.o build/temp.linux-i686-3.9/bcftools/consensus.c.pysam.o build/temp.linux-i686-3.9/bcftools/convert.c.pysam.o build/temp.linux-i686-3.9/bcftools/csq.c.pysam.o build/temp.linux-i686-3.9/bcftools/dist.c.pysam.o build/temp.linux-i686-3.9/bcftools/em.c.pysam.o build/temp.linux-i686-3.9/bcftools/extsort.c.pysam.o build/temp.linux-i686-3.9/bcftools/filter.c.pysam.o build/temp.linux-i686-3.9/bcftools/gvcf.c.pysam.o build/temp.linux-i686-3.9/bcftools/hclust.c.pysam.o build/temp.linux-i686-3.9/bcftools/kmin.c.pysam.o build/temp.linux-i686-3.9/bcftools/main.c.pysam.o build/temp.linux-i686-3.9/bcftools/mcall.c.pysam.o build/temp.linux-i686-3.9/bcftools/mpileup.c.pysam.o build/temp.linux-i686-3.9/bcftools/ploidy.c.pysam.o build/temp.linux-i686-3.9/bcftools/prob1.c.pysam.o build/temp.linux-i686-3.9/bcftools/regidx.c.pysam.o build/temp.linux-i686-3.9/bcftools/reheader.c.pysam.o build/temp.linux-i686-3.9/bcftools/smpl_ilist.c.pysam.o build/temp.linux-i686-3.9/bcftools/str_finder.c.pysam.o build/temp.linux-i686-3.9/bcftools/tabix.c.pysam.o build/temp.linux-i686-3.9/bcftools/tsv2vcf.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfannotate.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfbuf.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfcall.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfcnv.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfconcat.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfconvert.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcffilter.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfhead.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfindex.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfisec.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfmerge.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfnorm.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfplugin.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfquery.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfroh.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfsom.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfsort.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfstats.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcfview.c.pysam.o build/temp.linux-i686-3.9/bcftools/vcmp.c.pysam.o build/temp.linux-i686-3.9/bcftools/version.c.pysam.o build/temp.linux-i686-3.9/pysam/libcbcftools.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libcbcftools.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libcutils.c -o build/temp.linux-i686-3.9/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/pysam_util.c -o build/temp.linux-i686-3.9/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libcutils.o build/temp.linux-i686-3.9/pysam/pysam_util.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -lcsamtools.cpython-39-i386-linux-gnu -lcbcftools.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libcutils.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libcalignmentfile.c -o build/temp.linux-i686-3.9/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libcalignmentfile.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -lcutils.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libcalignmentfile.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libcsamfile.c -o build/temp.linux-i686-3.9/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libcsamfile.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -lcutils.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libcsamfile.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libcalignedsegment.c -o build/temp.linux-i686-3.9/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libcalignedsegment.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -lcutils.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libcalignedsegment.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libctabix.c -o build/temp.linux-i686-3.9/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libctabix.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -lcutils.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libctabix.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libcfaidx.c -o build/temp.linux-i686-3.9/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libcfaidx.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -lcutils.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libcfaidx.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libcbcf.c -o build/temp.linux-i686-3.9/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libcbcf.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -lcutils.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libcbcf.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libcbgzf.c -o build/temp.linux-i686-3.9/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libcbgzf.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -lcutils.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libcbgzf.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libctabixproxies.c -o build/temp.linux-i686-3.9/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libctabixproxies.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -lcutils.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libctabixproxies.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/samtools/lz4 -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/bcftools -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -I/usr/src/slapt-src/academic/pysam/pysam-0.19.0 -I/usr/include/python3.9 -c pysam/libcvcf.c -o build/temp.linux-i686-3.9/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -shared build/temp.linux-i686-3.9/pysam/libcvcf.o -L/usr/src/slapt-src/academic/pysam/pysam-0.19.0/pysam -L/usr/lib -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -Lbuild/lib.linux-i686-3.9/pysam -L/usr/lib -lz -lhts -lchtslib.cpython-39-i386-linux-gnu -lcutils.cpython-39-i386-linux-gnu -o build/lib.linux-i686-3.9/pysam/libcvcf.cpython-39-i386-linux-gnu.so -Wl,-rpath,$ORIGIN
running install_lib
creating /usr/src/slapt-src/academic/pysam/package-pysam/usr
creating /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib
creating /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9
creating /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages
creating /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/Pileup.py -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/__init__.py -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/bcftools.py -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/samtools.py -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/utils.py -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/version.py -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/config.py -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
creating /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include
copying build/lib.linux-i686-3.9/pysam/include/__init__.py -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include
creating /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/bam.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/bam_ampliconclip.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/bam_lpileup.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/bam_plbuf.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/bedidx.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/consensus_pileup.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/sam_opts.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/sample.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/samtools.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/samtools.pysam.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/splaysort.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/stats_isize.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/tmp_file.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
copying build/lib.linux-i686-3.9/pysam/include/samtools/config.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/samtools
creating /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/HMM.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/abuf.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/bam2bcf.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/bam_sample.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/bcftools.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/bcftools.pysam.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/bin.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/call.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/cols.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/convert.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/dist.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/extsort.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/filter.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/gvcf.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/hclust.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/hex.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/khash_str2str.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/kheap.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/kmin.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/mw.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/ploidy.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/prob1.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/rbuf.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/regidx.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/smpl_ilist.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/str_finder.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/tsv2vcf.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/utlist.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/variantkey.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/vcfbuf.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/vcmp.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying build/lib.linux-i686-3.9/pysam/include/bcftools/config.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/bcftools
creating /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/bcf_sr_sort.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/header.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/hfile_internal.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/hts_internal.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/sam_internal.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/textutils_internal.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/thread_pool_internal.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/config.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib
creating /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/bgzf.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/cram.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/faidx.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/hfile.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/hts.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/hts_defs.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/hts_endian.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/hts_expr.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/hts_log.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/hts_os.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/kbitset.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/kfunc.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/khash.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/khash_str2int.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/klist.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/knetfile.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/kroundup.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/kseq.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/ksort.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/kstring.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/regidx.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/sam.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/synced_bcf_reader.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/tbx.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/thread_pool.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/vcf.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/vcf_sweep.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/include/htslib/htslib/vcfutils.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/htslib/htslib
copying build/lib.linux-i686-3.9/pysam/libcalignedsegment.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcalignmentfile.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcbcf.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcbcftools.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcfaidx.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libchtslib.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcsamfile.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcsamtools.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libctabix.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libctabixproxies.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcutils.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcvcf.pxd -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/cbcftools_util.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/csamtools_util.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/htslib_util.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/pysam_stream.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/pysam_util.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/version.h -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/py.typed -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcalignedsegment.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcalignmentfile.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcbcf.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcbcftools.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcbgzf.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcfaidx.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libchtslib.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcsamfile.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcsamtools.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libctabix.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libctabixproxies.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcutils.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcvcf.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/version.pyi -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libchtslib.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcsamtools.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcbcftools.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcutils.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcalignmentfile.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcsamfile.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcalignedsegment.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libctabix.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcfaidx.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcbcf.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcbgzf.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libctabixproxies.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
copying build/lib.linux-i686-3.9/pysam/libcvcf.cpython-39-i386-linux-gnu.so -> /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam
byte-compiling /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/Pileup.py to Pileup.cpython-39.pyc
byte-compiling /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/__init__.py to __init__.cpython-39.pyc
byte-compiling /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/bcftools.py to bcftools.cpython-39.pyc
byte-compiling /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/samtools.py to samtools.cpython-39.pyc
byte-compiling /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/utils.py to utils.cpython-39.pyc
byte-compiling /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/version.py to version.cpython-39.pyc
byte-compiling /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/config.py to config.cpython-39.pyc
byte-compiling /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam/include/__init__.py to __init__.cpython-39.pyc
running install_egg_info
running egg_info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing top-level names to pysam.egg-info/top_level.txt
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'COPYING'
adding license file 'AUTHORS'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /usr/src/slapt-src/academic/pysam/package-pysam/usr/lib/python3.9/site-packages/pysam-0.19.0-py3.9.egg-info
running install_scripts

Slackware package maker, version 3.14159265.

Searching for symbolic links:

No symbolic links were found, so we won't make an installation script.
You can make your own later in ./install/doinst.sh and rebuild the
package if you like.

This next step is optional - you can set the directories in your package
to some sane permissions. If any of the directories in your package have
special permissions, then DO NOT reset them here!

Would you like to reset all directory permissions to 755 (drwxr-xr-x) and
directory ownerships to root.root ([y]es, [n]o)? n

Creating Slackware package:  /usr/src/slapt-src/academic/pysam/pysam-0.19.0-i586-1salix15.0.txz

WARNING:  zero length file usr/lib/python3.9/site-packages/pysam/include/__init__.py
WARNING:  zero length file usr/lib/python3.9/site-packages/pysam/py.typed
WARNING:  zero length file usr/lib/python3.9/site-packages/pysam/libcvcf.pyi

Slackware package /usr/src/slapt-src/academic/pysam/pysam-0.19.0-i586-1salix15.0.txz created.

Installing package pysam-0.19.0-i586-1salix15.0...
| pysam (read/write genomic data sets)
| 
| Pysam is a python module for reading and manipulating files in the
| SAM, BAM, CRAM, VCF, and BCF format used for storing and writing
| genomic data sets. Pysam is a lightweight wrapper of the samtools
| and htslib C-API's and also includes an interface for tabix.
| 
| Home: https://github.com/pysam-developers/pysam
| Howto: https://pysam.readthedocs.io/en/latest/
| 
| 
| 
| 
ysam/__init__.py
usr/lib/python3.9/site-packages/pysam/__pycache__/
usr/lib/python3.9/site-packages/pysam/__pycache__/Pileup.cpython-39.pyc
usr/lib/python3.9/site-packages/pysam/__pycache__/__init__.cpython-39.pyc
usr/lib/python3.9/site-packages/pysam/__pycache__/bcftools.cpython-39.pyc
usr/lib/python3.9/site-packages/pysam/__pycache__/config.cpython-39.pyc
usr/lib/python3.9/site-packages/pysam/__pycache__/samtools.cpython-39.pyc
usr/lib/python3.9/site-packages/pysam/__pycache__/utils.cpython-39.pyc
usr/lib/python3.9/site-packages/pysam/__pycache__/version.cpython-39.pyc
usr/lib/python3.9/site-packages/pysam/bcftools.py
usr/lib/python3.9/site-packages/pysam/cbcftools_util.h
usr/lib/python3.9/site-packages/pysam/config.py
usr/lib/python3.9/site-packages/pysam/csamtools_util.h
usr/lib/python3.9/site-packages/pysam/htslib_util.h
usr/lib/python3.9/site-packages/pysam/include/
usr/lib/python3.9/site-packages/pysam/include/__init__.py
usr/lib/python3.9/site-packages/pysam/include/__pycache__/
usr/lib/python3.9/site-packages/pysam/include/__pycache__/__init__.cpython-39.pyc
usr/lib/python3.9/site-packages/pysam/include/bcftools/
usr/lib/python3.9/site-packages/pysam/include/bcftools/HMM.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/abuf.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/bam2bcf.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/bam_sample.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/bcftools.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/bcftools.pysam.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/bin.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/call.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/cols.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/config.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/convert.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/dist.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/extsort.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/filter.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/gvcf.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/hclust.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/hex.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/khash_str2str.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/kheap.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/kmin.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/mw.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/ploidy.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/prob1.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/rbuf.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/regidx.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/smpl_ilist.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/str_finder.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/tsv2vcf.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/utlist.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/variantkey.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/vcfbuf.h
usr/lib/python3.9/site-packages/pysam/include/bcftools/vcmp.h
usr/lib/python3.9/site-packages/pysam/include/htslib/
usr/lib/python3.9/site-packages/pysam/include/htslib/bcf_sr_sort.h
usr/lib/python3.9/site-packages/pysam/include/htslib/config.h
usr/lib/python3.9/site-packages/pysam/include/htslib/header.h
usr/lib/python3.9/site-packages/pysam/include/htslib/hfile_internal.h
usr/lib/python3.9/site-packages/pysam/include/htslib/hts_internal.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/bgzf.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/cram.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/faidx.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/hfile.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/hts.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/hts_defs.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/hts_endian.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/hts_expr.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/hts_log.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/hts_os.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/kbitset.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/kfunc.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/khash.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/khash_str2int.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/klist.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/knetfile.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/kroundup.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/kseq.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/ksort.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/kstring.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/regidx.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/sam.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/synced_bcf_reader.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/tbx.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/thread_pool.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcf.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcf_sweep.h
usr/lib/python3.9/site-packages/pysam/include/htslib/htslib/vcfutils.h
usr/lib/python3.9/site-packages/pysam/include/htslib/sam_internal.h
usr/lib/python3.9/site-packages/pysam/include/htslib/textutils_internal.h
usr/lib/python3.9/site-packages/pysam/include/htslib/thread_pool_internal.h
usr/lib/python3.9/site-packages/pysam/include/samtools/
usr/lib/python3.9/site-packages/pysam/include/samtools/bam.h
usr/lib/python3.9/site-packages/pysam/include/samtools/bam_ampliconclip.h
usr/lib/python3.9/site-packages/pysam/include/samtools/bam_lpileup.h
usr/lib/python3.9/site-packages/pysam/include/samtools/bam_plbuf.h
usr/lib/python3.9/site-packages/pysam/include/samtools/bedidx.h
usr/lib/python3.9/site-packages/pysam/include/samtools/config.h
usr/lib/python3.9/site-packages/pysam/include/samtools/consensus_pileup.h
usr/lib/python3.9/site-packages/pysam/include/samtools/sam_opts.h
usr/lib/python3.9/site-packages/pysam/include/samtools/sample.h
usr/lib/python3.9/site-packages/pysam/include/samtools/samtools.h
usr/lib/python3.9/site-packages/pysam/include/samtools/samtools.pysam.h
usr/lib/python3.9/site-packages/pysam/include/samtools/splaysort.h
usr/lib/python3.9/site-packages/pysam/include/samtools/stats_isize.h
usr/lib/python3.9/site-packages/pysam/include/samtools/tmp_file.h
usr/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libcalignedsegment.pxd
usr/lib/python3.9/site-packages/pysam/libcalignedsegment.pyi
usr/lib/python3.9/site-packages/pysam/libcalignmentfile.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libcalignmentfile.pxd
usr/lib/python3.9/site-packages/pysam/libcalignmentfile.pyi
usr/lib/python3.9/site-packages/pysam/libcbcf.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libcbcf.pxd
usr/lib/python3.9/site-packages/pysam/libcbcf.pyi
usr/lib/python3.9/site-packages/pysam/libcbcftools.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libcbcftools.pxd
usr/lib/python3.9/site-packages/pysam/libcbcftools.pyi
usr/lib/python3.9/site-packages/pysam/libcbgzf.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libcbgzf.pyi
usr/lib/python3.9/site-packages/pysam/libcfaidx.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libcfaidx.pxd
usr/lib/python3.9/site-packages/pysam/libcfaidx.pyi
usr/lib/python3.9/site-packages/pysam/libchtslib.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libchtslib.pxd
usr/lib/python3.9/site-packages/pysam/libchtslib.pyi
usr/lib/python3.9/site-packages/pysam/libcsamfile.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libcsamfile.pxd
usr/lib/python3.9/site-packages/pysam/libcsamfile.pyi
usr/lib/python3.9/site-packages/pysam/libcsamtools.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libcsamtools.pxd
usr/lib/python3.9/site-packages/pysam/libcsamtools.pyi
usr/lib/python3.9/site-packages/pysam/libctabix.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libctabix.pxd
usr/lib/python3.9/site-packages/pysam/libctabix.pyi
usr/lib/python3.9/site-packages/pysam/libctabixproxies.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libctabixproxies.pxd
usr/lib/python3.9/site-packages/pysam/libctabixproxies.pyi
usr/lib/python3.9/site-packages/pysam/libcutils.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libcutils.pxd
usr/lib/python3.9/site-packages/pysam/libcutils.pyi
usr/lib/python3.9/site-packages/pysam/libcvcf.cpython-39-i386-linux-gnu.so
usr/lib/python3.9/site-packages/pysam/libcvcf.pxd
usr/lib/python3.9/site-packages/pysam/libcvcf.pyi
usr/lib/python3.9/site-packages/pysam/py.typed
usr/lib/python3.9/site-packages/pysam/pysam_stream.h
usr/lib/python3.9/site-packages/pysam/pysam_util.h
usr/lib/python3.9/site-packages/pysam/samtools.py
usr/lib/python3.9/site-packages/pysam/utils.py
usr/lib/python3.9/site-packages/pysam/version.h
usr/lib/python3.9/site-packages/pysam/version.py
usr/lib/python3.9/site-packages/pysam/version.pyi