tests/AlignmentFile_test.py | 1 1 + 0 - 0 !
tests/tabix_test.py | 42 23 + 19 - 0 !
2 files changed, 24 insertions(+), 19 deletions(-)

 skip tests trying to access remote site

bcftools/filter.c | 2 1 + 1 - 0 !
bcftools/filter.c.pysam.c | 2 1 + 1 - 0 !
pysam/libcalignedsegment.pyx | 2 1 + 1 - 0 !
pysam/libcalignmentfile.pyx | 8 4 + 4 - 0 !
pysam/libchtslib.pxd | 2 1 + 1 - 0 !
pysam/libchtslib.pyx | 4 2 + 2 - 0 !
pysam/libcutils.pyx | 2 1 + 1 - 0 !
7 files changed, 11 insertions(+), 11 deletions(-)

 fix spelling typos, courtesy of lintian

pysam/htslib_util.h | 3 0 + 3 - 0 !
pysam/libchtslib.pxd | 2 0 + 2 - 0 !
pysam/libchtslib.pyx | 6 2 + 4 - 0 !
setup.py | 3 1 + 2 - 0 !
tests/00README.txt | 2 1 + 1 - 0 !
tests/pysam_data/Makefile | 6 3 + 3 - 0 !
6 files changed, 7 insertions(+), 15 deletions(-)

 sync with htslib, samtools, and bcftools 1.10

- Remove symbols that was removed in libhts3 (hts_useek and uts_utell)
- use devtools/import.py and the contents of the samtools & bcftools 1.10
Debian packages with their patches fully applied

pysam/alternatives.py.obsolete | 1 0 + 1 - 0 !
samtools/LICENSE | 2 1 + 1 - 0 !
samtools/README | 10 5 + 5 - 0 !
samtools/bam.c | 60 13 + 47 - 0 !
samtools/bam.c.pysam.c | 60 13 + 47 - 0 !
samtools/bam.h | 20 5 + 15 - 0 !
samtools/bam2bcf.c | 2 1 + 1 - 0 !
samtools/bam2bcf.c.pysam.c | 2 1 + 1 - 0 !
samtools/bam2bcf.h | 7 4 + 3 - 0 !
samtools/bam2bcf_indel.c | 24 14 + 10 - 0 !
samtools/bam2bcf_indel.c.pysam.c | 24 14 + 10 - 0 !
samtools/bam2depth.c | 184 134 + 50 - 0 !
samtools/bam2depth.c.pysam.c | 184 134 + 50 - 0 !
samtools/bam_addrprg.c | 141 65 + 76 - 0 !
samtools/bam_addrprg.c.pysam.c | 141 65 + 76 - 0 !
samtools/bam_aux.c | 26 10 + 16 - 0 !
samtools/bam_aux.c.pysam.c | 26 10 + 16 - 0 !
samtools/bam_cat.c | 348 152 + 196 - 0 !
samtools/bam_cat.c.pysam.c | 348 152 + 196 - 0 !
samtools/bam_fastq.c | 1037 1037 + 0 - 0 !
samtools/bam_fastq.c.pysam.c | 1039 1039 + 0 - 0 !
samtools/bam_import.c | 65 0 + 65 - 0 !
samtools/bam_import.c.pysam.c | 67 0 + 67 - 0 !
samtools/bam_index.c | 26 13 + 13 - 0 !
samtools/bam_index.c.pysam.c | 26 13 + 13 - 0 !
samtools/bam_lpileup.c | 2 1 + 1 - 0 !
samtools/bam_lpileup.c.pysam.c | 2 1 + 1 - 0 !
samtools/bam_lpileup.h | 2 1 + 1 - 0 !
samtools/bam_markdup.c | 1277 1059 + 218 - 0 !
samtools/bam_markdup.c.pysam.c | 1277 1059 + 218 - 0 !
samtools/bam_mate.c | 75 46 + 29 - 0 !
samtools/bam_mate.c.pysam.c | 75 46 + 29 - 0 !
samtools/bam_md.c | 50 35 + 15 - 0 !
samtools/bam_md.c.pysam.c | 50 35 + 15 - 0 !
samtools/bam_plbuf.c | 5 3 + 2 - 0 !
samtools/bam_plbuf.c.pysam.c | 5 3 + 2 - 0 !
samtools/bam_plbuf.h | 2 1 + 1 - 0 !
samtools/bam_plcmd.c | 456 345 + 111 - 0 !
samtools/bam_plcmd.c.pysam.c | 456 345 + 111 - 0 !
samtools/bam_quickcheck.c | 18 11 + 7 - 0 !
samtools/bam_quickcheck.c.pysam.c | 18 11 + 7 - 0 !
samtools/bam_reheader.c | 271 193 + 78 - 0 !
samtools/bam_reheader.c.pysam.c | 271 193 + 78 - 0 !
samtools/bam_rmdup.c | 23 13 + 10 - 0 !
samtools/bam_rmdup.c.pysam.c | 23 13 + 10 - 0 !
samtools/bam_rmdupse.c | 13 8 + 5 - 0 !
samtools/bam_rmdupse.c.pysam.c | 13 8 + 5 - 0 !
samtools/bam_sort.c | 852 411 + 441 - 0 !
samtools/bam_sort.c.pysam.c | 852 411 + 441 - 0 !
samtools/bam_split.c | 341 163 + 178 - 0 !
samtools/bam_split.c.pysam.c | 341 163 + 178 - 0 !
samtools/bam_stat.c | 170 149 + 21 - 0 !
samtools/bam_stat.c.pysam.c | 170 149 + 21 - 0 !
samtools/bamshuf.c | 54 34 + 20 - 0 !
samtools/bamshuf.c.pysam.c | 54 34 + 20 - 0 !
samtools/bamtk.c | 23 15 + 8 - 0 !
samtools/bamtk.c.pysam.c | 21 14 + 7 - 0 !
samtools/bedcov.c | 40 31 + 9 - 0 !
samtools/bedcov.c.pysam.c | 40 31 + 9 - 0 !
samtools/bedidx.c | 120 70 + 50 - 0 !
samtools/bedidx.c.pysam.c | 120 70 + 50 - 0 !
samtools/bedidx.h | 2 1 + 1 - 0 !
samtools/coverage.c | 702 702 + 0 - 0 !
samtools/coverage.c.pysam.c | 704 704 + 0 - 0 !
samtools/cut_target.c | 32 17 + 15 - 0 !
samtools/cut_target.c.pysam.c | 32 17 + 15 - 0 !
samtools/dict.c | 1 1 + 0 - 0 !
samtools/dict.c.pysam.c | 1 1 + 0 - 0 !
samtools/faidx.c | 39 21 + 18 - 0 !
samtools/faidx.c.pysam.c | 39 21 + 18 - 0 !
samtools/htslib-1.9/LICENSE | 69 0 + 69 - 0 !
samtools/htslib-1.9/README | 5 0 + 5 - 0 !
samtools/misc/ace2sam.c | 3 2 + 1 - 0 !
samtools/misc/ace2sam.c.pysam.c | 3 2 + 1 - 0 !
samtools/padding.c | 249 109 + 140 - 0 !
samtools/padding.c.pysam.c | 249 109 + 140 - 0 !
samtools/phase.c | 51 37 + 14 - 0 !
samtools/phase.c.pysam.c | 51 37 + 14 - 0 !
samtools/sam.c | 8 4 + 4 - 0 !
samtools/sam.c.pysam.c | 8 4 + 4 - 0 !
samtools/sam.h | 16 11 + 5 - 0 !
samtools/sam_header.c | 836 0 + 836 - 0 !
samtools/sam_header.c.pysam.c | 838 0 + 838 - 0 !
samtools/sam_header.h | 72 0 + 72 - 0 !
samtools/sam_opts.c | 51 42 + 9 - 0 !
samtools/sam_opts.c.pysam.c | 51 42 + 9 - 0 !
samtools/sam_opts.h | 12 7 + 5 - 0 !
samtools/sam_utils.c | 80 79 + 1 - 0 !
samtools/sam_utils.c.pysam.c | 80 79 + 1 - 0 !
samtools/sam_view.c | 1234 247 + 987 - 0 !
samtools/sam_view.c.pysam.c | 1234 247 + 987 - 0 !
samtools/samtools.h | 25 19 + 6 - 0 !
samtools/stats.c | 809 564 + 245 - 0 !
samtools/stats.c.pysam.c | 809 564 + 245 - 0 !
samtools/stats_isize.c | 24 21 + 3 - 0 !
samtools/stats_isize.c.pysam.c | 24 21 + 3 - 0 !
samtools/test/merge/test_bam_translate.c | 15 8 + 7 - 0 !
samtools/test/merge/test_bam_translate.c.pysam.c | 15 8 + 7 - 0 !
samtools/test/merge/test_trans_tbl_init.c | 176 81 + 95 - 0 !
samtools/test/merge/test_trans_tbl_init.c.pysam.c | 176 81 + 95 - 0 !
samtools/test/split/test_count_rg.c | 26 13 + 13 - 0 !
samtools/test/split/test_count_rg.c.pysam.c | 26 13 + 13 - 0 !
samtools/test/split/test_expand_format_string.c | 7 3 + 4 - 0 !
samtools/test/split/test_expand_format_string.c.pysam.c | 7 3 + 4 - 0 !
samtools/test/split/test_filter_header_rg.c | 198 160 + 38 - 0 !
samtools/test/split/test_filter_header_rg.c.pysam.c | 198 160 + 38 - 0 !
samtools/test/test.c | 37 30 + 7 - 0 !
samtools/test/test.c.pysam.c | 37 30 + 7 - 0 !
samtools/test/test.h | 5 4 + 1 - 0 !
samtools/tmp_file.c | 129 30 + 99 - 0 !
samtools/tmp_file.c.pysam.c | 129 30 + 99 - 0 !
samtools/tmp_file.h | 40 10 + 30 - 0 !
samtools/version.h | 2 1 + 1 - 0 !
samtools/win32/xcurses.h | 1377 0 + 1377 - 0 !
samtools/win32/zconf.h | 332 0 + 332 - 0 !
samtools/win32/zlib.h | 1357 0 + 1357 - 0 !
tests/AlignmentFile_test.py | 26 13 + 13 - 0 !
tests/pysam_data/Makefile | 1 0 + 1 - 0 !
tests/pysam_data/example_empty_with_header.sam | 1 0 + 1 - 0 !
tests/pysam_data/example_user_header.sam | 8 0 + 8 - 0 !
tests/pysam_data/rg_with_tab.sam | 3273 0 + 3273 - 0 !
tests/samtools_test.py | 6 3 + 3 - 0 !
122 files changed, 12483 insertions(+), 15016 deletions(-)

 sync with samtools 1.10

use devtools/import.py and the contents of the samtools
Debian package with its patches fully applied

bcftools/LICENSE | 23 23 + 0 - 0 !
bcftools/bam2bcf.c | 33 28 + 5 - 0 !
bcftools/bam2bcf.c.pysam.c | 33 28 + 5 - 0 !
bcftools/bam2bcf.h | 14 12 + 2 - 0 !
bcftools/bcftools.h | 8 8 + 0 - 0 !
bcftools/call.h | 36 32 + 4 - 0 !
bcftools/cols.c | 109 109 + 0 - 0 !
bcftools/cols.c.pysam.c | 111 111 + 0 - 0 !
bcftools/cols.h | 51 51 + 0 - 0 !
bcftools/consensus.c | 112 78 + 34 - 0 !
bcftools/consensus.c.pysam.c | 112 78 + 34 - 0 !
bcftools/convert.c | 278 243 + 35 - 0 !
bcftools/convert.c.pysam.c | 278 243 + 35 - 0 !
bcftools/csq.c | 580 454 + 126 - 0 !
bcftools/csq.c.pysam.c | 580 454 + 126 - 0 !
bcftools/filter.c | 392 314 + 78 - 0 !
bcftools/filter.c.pysam.c | 392 314 + 78 - 0 !
bcftools/gvcf.c | 2 1 + 1 - 0 !
bcftools/gvcf.c.pysam.c | 2 1 + 1 - 0 !
bcftools/hex.h | 95 95 + 0 - 0 !
bcftools/htslib-1.9/LICENSE | 69 0 + 69 - 0 !
bcftools/htslib-1.9/README | 5 0 + 5 - 0 !
bcftools/main.c | 23 17 + 6 - 0 !
bcftools/main.c.pysam.c | 23 17 + 6 - 0 !
bcftools/mcall.c | 390 265 + 125 - 0 !
bcftools/mcall.c.pysam.c | 390 265 + 125 - 0 !
bcftools/mpileup.c | 97 68 + 29 - 0 !
bcftools/mpileup.c.pysam.c | 97 68 + 29 - 0 !
bcftools/plugins/GTisec.c | 2 1 + 1 - 0 !
bcftools/plugins/GTisec.c.pysam.c | 2 1 + 1 - 0 !
bcftools/plugins/GTsubset.c | 2 1 + 1 - 0 !
bcftools/plugins/GTsubset.c.pysam.c | 2 1 + 1 - 0 !
bcftools/plugins/ad-bias.c | 110 91 + 19 - 0 !
bcftools/plugins/ad-bias.c.pysam.c | 110 91 + 19 - 0 !
bcftools/plugins/add-variantkey.c | 86 86 + 0 - 0 !
bcftools/plugins/add-variantkey.c.pysam.c | 88 88 + 0 - 0 !
bcftools/plugins/af-dist.c | 4 2 + 2 - 0 !
bcftools/plugins/af-dist.c.pysam.c | 4 2 + 2 - 0 !
bcftools/plugins/allele-length.c | 113 113 + 0 - 0 !
bcftools/plugins/allele-length.c.pysam.c | 115 115 + 0 - 0 !
bcftools/plugins/check-ploidy.c | 4 2 + 2 - 0 !
bcftools/plugins/check-ploidy.c.pysam.c | 4 2 + 2 - 0 !
bcftools/plugins/check-sparsity.c | 4 2 + 2 - 0 !
bcftools/plugins/check-sparsity.c.pysam.c | 4 2 + 2 - 0 !
bcftools/plugins/contrast.c | 328 244 + 84 - 0 !
bcftools/plugins/contrast.c.pysam.c | 328 244 + 84 - 0 !
bcftools/plugins/counts.c | 17 9 + 8 - 0 !
bcftools/plugins/counts.c.pysam.c | 17 9 + 8 - 0 !
bcftools/plugins/dosage.c | 24 14 + 10 - 0 !
bcftools/plugins/dosage.c.pysam.c | 24 14 + 10 - 0 !
bcftools/plugins/fill-AN-AC.c | 2 1 + 1 - 0 !
bcftools/plugins/fill-AN-AC.c.pysam.c | 2 1 + 1 - 0 !
bcftools/plugins/fill-from-fasta.c | 15 12 + 3 - 0 !
bcftools/plugins/fill-from-fasta.c.pysam.c | 15 12 + 3 - 0 !
bcftools/plugins/fill-tags.c | 264 200 + 64 - 0 !
bcftools/plugins/fill-tags.c.pysam.c | 264 200 + 64 - 0 !
bcftools/plugins/fixploidy.c | 6 3 + 3 - 0 !
bcftools/plugins/fixploidy.c.pysam.c | 6 3 + 3 - 0 !
bcftools/plugins/fixref.c | 42 30 + 12 - 0 !
bcftools/plugins/fixref.c.pysam.c | 42 30 + 12 - 0 !
bcftools/plugins/guess-ploidy.c | 4 2 + 2 - 0 !
bcftools/plugins/guess-ploidy.c.pysam.c | 4 2 + 2 - 0 !
bcftools/plugins/gvcfz.c | 378 378 + 0 - 0 !
bcftools/plugins/gvcfz.c.pysam.c | 380 380 + 0 - 0 !
bcftools/plugins/indel-stats.c | 753 753 + 0 - 0 !
bcftools/plugins/indel-stats.c.pysam.c | 755 755 + 0 - 0 !
bcftools/plugins/isecGT.c | 6 3 + 3 - 0 !
bcftools/plugins/isecGT.c.pysam.c | 6 3 + 3 - 0 !
bcftools/plugins/mendelian.c | 44 28 + 16 - 0 !
bcftools/plugins/mendelian.c.pysam.c | 44 28 + 16 - 0 !
bcftools/plugins/missing2ref.c | 2 1 + 1 - 0 !
bcftools/plugins/missing2ref.c.pysam.c | 2 1 + 1 - 0 !
bcftools/plugins/parental-origin.c | 410 410 + 0 - 0 !
bcftools/plugins/parental-origin.c.pysam.c | 412 412 + 0 - 0 !
bcftools/plugins/prune.c | 10 5 + 5 - 0 !
bcftools/plugins/prune.c.pysam.c | 10 5 + 5 - 0 !
bcftools/plugins/remove-overlaps.c | 219 219 + 0 - 0 !
bcftools/plugins/remove-overlaps.c.pysam.c | 221 221 + 0 - 0 !
bcftools/plugins/setGT.c | 8 4 + 4 - 0 !
bcftools/plugins/setGT.c.pysam.c | 8 4 + 4 - 0 !
bcftools/plugins/smpl-stats.c | 9 5 + 4 - 0 !
bcftools/plugins/smpl-stats.c.pysam.c | 9 5 + 4 - 0 !
bcftools/plugins/split-vep.c | 934 934 + 0 - 0 !
bcftools/plugins/split-vep.c.pysam.c | 936 936 + 0 - 0 !
bcftools/plugins/split.c | 77 54 + 23 - 0 !
bcftools/plugins/split.c.pysam.c | 77 54 + 23 - 0 !
bcftools/plugins/tag2tag.c | 5 3 + 2 - 0 !
bcftools/plugins/tag2tag.c.pysam.c | 5 3 + 2 - 0 !
bcftools/plugins/trio-dnm.c | 444 444 + 0 - 0 !
bcftools/plugins/trio-dnm.c.pysam.c | 446 446 + 0 - 0 !
bcftools/plugins/trio-stats.c | 327 268 + 59 - 0 !
bcftools/plugins/trio-stats.c.pysam.c | 327 268 + 59 - 0 !
bcftools/plugins/trio-switch-rate.c | 2 1 + 1 - 0 !
bcftools/plugins/trio-switch-rate.c.pysam.c | 2 1 + 1 - 0 !
bcftools/plugins/variantkey-hex.c | 136 136 + 0 - 0 !
bcftools/plugins/variantkey-hex.c.pysam.c | 138 138 + 0 - 0 !
bcftools/regidx.c | 11 7 + 4 - 0 !
bcftools/regidx.c.pysam.c | 11 7 + 4 - 0 !
bcftools/regidx.h | 10 5 + 5 - 0 !
bcftools/reheader.c | 213 194 + 19 - 0 !
bcftools/reheader.c.pysam.c | 213 194 + 19 - 0 !
bcftools/smpl_ilist.c | 66 56 + 10 - 0 !
bcftools/smpl_ilist.c.pysam.c | 66 56 + 10 - 0 !
bcftools/smpl_ilist.h | 11 8 + 3 - 0 !
bcftools/tabix.c | 2 1 + 1 - 0 !
bcftools/tabix.c.pysam.c | 2 1 + 1 - 0 !
bcftools/test/test-regidx.c | 70 70 + 0 - 0 !
bcftools/test/test-regidx.c.pysam.c | 70 70 + 0 - 0 !
bcftools/variantkey.h | 583 583 + 0 - 0 !
bcftools/vcfannotate.c | 878 672 + 206 - 0 !
bcftools/vcfannotate.c.pysam.c | 878 672 + 206 - 0 !
bcftools/vcfbuf.c | 52 44 + 8 - 0 !
bcftools/vcfbuf.c.pysam.c | 52 44 + 8 - 0 !
bcftools/vcfbuf.h | 15 14 + 1 - 0 !
bcftools/vcfcall.c | 342 300 + 42 - 0 !
bcftools/vcfcall.c.pysam.c | 342 300 + 42 - 0 !
bcftools/vcfcnv.c | 20 11 + 9 - 0 !
bcftools/vcfcnv.c.pysam.c | 20 11 + 9 - 0 !
bcftools/vcfconcat.c | 257 200 + 57 - 0 !
bcftools/vcfconcat.c.pysam.c | 257 200 + 57 - 0 !
bcftools/vcfconvert.c | 59 33 + 26 - 0 !
bcftools/vcfconvert.c.pysam.c | 59 33 + 26 - 0 !
bcftools/vcffilter.c | 30 20 + 10 - 0 !
bcftools/vcffilter.c.pysam.c | 30 20 + 10 - 0 !
bcftools/vcfgtcheck.c | 15 8 + 7 - 0 !
bcftools/vcfgtcheck.c.pysam.c | 15 8 + 7 - 0 !
bcftools/vcfindex.c | 4 2 + 2 - 0 !
bcftools/vcfindex.c.pysam.c | 4 2 + 2 - 0 !
bcftools/vcfisec.c | 43 29 + 14 - 0 !
bcftools/vcfisec.c.pysam.c | 43 29 + 14 - 0 !
bcftools/vcfmerge.c | 304 240 + 64 - 0 !
bcftools/vcfmerge.c.pysam.c | 304 240 + 64 - 0 !
bcftools/vcfnorm.c | 292 210 + 82 - 0 !
bcftools/vcfnorm.c.pysam.c | 292 210 + 82 - 0 !
bcftools/vcfplugin.c | 121 106 + 15 - 0 !
bcftools/vcfplugin.c.pysam.c | 121 106 + 15 - 0 !
bcftools/vcfquery.c | 24 15 + 9 - 0 !
bcftools/vcfquery.c.pysam.c | 24 15 + 9 - 0 !
bcftools/vcfroh.c | 35 20 + 15 - 0 !
bcftools/vcfroh.c.pysam.c | 35 20 + 15 - 0 !
bcftools/vcfsom.c | 5 3 + 2 - 0 !
bcftools/vcfsom.c.pysam.c | 5 3 + 2 - 0 !
bcftools/vcfsort.c | 123 85 + 38 - 0 !
bcftools/vcfsort.c.pysam.c | 123 85 + 38 - 0 !
bcftools/vcfstats.c | 171 142 + 29 - 0 !
bcftools/vcfstats.c.pysam.c | 171 142 + 29 - 0 !
bcftools/vcfview.c | 27 16 + 11 - 0 !
bcftools/vcfview.c.pysam.c | 27 16 + 11 - 0 !
bcftools/version.c | 17 17 + 0 - 0 !
bcftools/version.c.pysam.c | 17 17 + 0 - 0 !
bcftools/version.h | 2 1 + 1 - 0 !
151 files changed, 17926 insertions(+), 2992 deletions(-)

 sync with bcftools 1.10

use devtools/import.py and the contents of the bcftools
Debian package with its patches fully applied

tests/pysam_data/Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

---