[med-svn] [bcftools] 02/06: Merge tag 'upstream/1.4.1'
Andreas Tille
tille at debian.org
Sun Jun 18 20:00:10 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bcftools.
commit 7f0275f5d4676a435dcd288a3c2ef07b10b98b8f
Merge: f9a9e80 0fb5584
Author: Andreas Tille <tille at debian.org>
Date: Sun Jun 18 21:40:20 2017 +0200
Merge tag 'upstream/1.4.1'
Upstream version 1.4.1
HMM.c | 141 +-
HMM.h | 26 +-
INSTALL | 24 +-
Makefile | 95 +-
NEWS | 236 +
bam2bcf.c | 857 +++
bam2bcf.h | 138 +
bam2bcf_indel.c | 470 ++
bam_sample.c | 393 ++
bam_sample.h | 50 +
bcftools.h | 1 +
bin.c | 104 +
bin.h | 65 +
call.h | 3 +-
ccall.c | 10 +-
consensus.c | 56 +-
convert.c | 490 +-
csq.c | 3824 +++++++++++++
doc/bcftools.1 | 1403 ++++-
doc/bcftools.html | 919 +++-
doc/bcftools.txt | 989 +++-
filter.c | 357 +-
hclust.c | 400 ++
hclust.h | 77 +
kheap.h | 171 +
main.c | 10 +
mcall.c | 228 +-
{plugins => misc}/color-chrs.pl | 0
misc/guess-ploidy.py | 117 +
misc/plot-roh.py | 253 +
plot-vcfstats => misc/plot-vcfstats | 294 +-
misc/run-roh.pl | 308 ++
vcfutils.pl => misc/vcfutils.pl | 0
mpileup.c | 1110 ++++
mw.h | 1944 +++++++
ploidy.c | 22 +-
ploidy.h | 2 +-
plugins/GTsubset.c | 266 +
plugins/GTsubset.mk | 2 +
plugins/ad-bias.c | 226 +
plugins/ad-bias.mk | 2 +
plugins/af-dist.c | 220 +
plugins/af-dist.mk | 2 +
plugins/check-sparsity.c | 273 +
plugins/color-chrs.c | 4 +-
plugins/fill-from-fasta.c | 206 +
plugins/fill-from-fasta.mk | 2 +
plugins/fill-tags.c | 545 +-
plugins/fixploidy.c | 1 +
plugins/fixref.c | 576 ++
plugins/guess-ploidy.c | 568 ++
plugins/impute-info.c | 2 +
plugins/isecGT.c | 177 +
plugins/mendelian.c | 12 +-
plugins/setGT.c | 148 +-
plugins/setGT.mk | 2 +
plugins/tag2tag.c | 146 +-
plugins/trio-switch-rate.c | 273 +
plugins/vcf2sex.c | 511 --
plugins/vcf2sex.mk | 2 -
prob1.c | 12 +-
prob1.h | 2 +-
regidx.c | 598 ++
regidx.h | 191 +
reheader.c | 6 +-
smpl_ilist.c | 106 +
smpl_ilist.h | 47 +
tabix.c | 30 +-
test/aa.fa | 29 +
test/aa.fa.fai | 8 +
test/aa.hdr | 1 +
test/aa.out | 31 +
test/aa.vcf | 30 +
test/ad-bias.out | 25 +
test/ad-bias.samples | 2 +
test/ad-bias.vcf | 42 +
test/af-dist.out | 23 +
test/af-dist.vcf | 19 +
test/annotate11.out | 18 +
test/annotate12.out | 20 +
test/annotate13.out | 15 +
test/annots11.tab | 4 +
test/check.chk | 12 +-
test/check_merge.chk | 6 +-
test/csq.1.out | 99 +
test/csq.fa | 34 +
test/csq.fa.fai | 3 +
test/csq.gff3 | 40 +
test/csq.vcf | 40 +
test/csq/ENSG00000173376/ENSG00000173376.fa | 626 +++
test/csq/ENSG00000173376/ENSG00000173376.fa.fai | 1 +
test/csq/ENSG00000173376/ENSG00000173376.gff | 22 +
test/csq/ENSG00000173376/synon.txt | 3 +
test/csq/ENSG00000173376/synon.vcf | 7 +
test/csq/ENST00000218032/ENST00000218032.fa | 278 +
test/csq/ENST00000218032/ENST00000218032.fa.fai | 1 +
test/csq/ENST00000218032/ENST00000218032.gff | 8 +
test/csq/ENST00000218032/start-lost.txt | 3 +
test/csq/ENST00000218032/start-lost.txt-l | 3 +
test/csq/ENST00000218032/start-lost.vcf | 6 +
test/csq/ENST00000227471/ENST00000227471.fa | 233 +
test/csq/ENST00000227471/ENST00000227471.fa.fai | 1 +
test/csq/ENST00000227471/ENST00000227471.gff | 28 +
.../insert-splice-vs-frameshift.txt | 3 +
.../insert-splice-vs-frameshift.vcf | 7 +
test/csq/ENST00000256452/ENST00000256452.fa | 953 ++++
test/csq/ENST00000256452/ENST00000256452.fa.fai | 1 +
test/csq/ENST00000256452/ENST00000256452.gff | 30 +
test/csq/ENST00000256452/intron.txt | 3 +
test/csq/ENST00000256452/intron.vcf | 7 +
test/csq/ENST00000294661/ENST00000294661.fa | 163 +
test/csq/ENST00000294661/ENST00000294661.fa.fai | 1 +
test/csq/ENST00000294661/ENST00000294661.gff | 6 +
test/csq/ENST00000294661/non-coding-boundary.txt | 3 +
test/csq/ENST00000294661/non-coding-boundary.txt-l | 3 +
test/csq/ENST00000294661/non-coding-boundary.vcf | 6 +
test/csq/ENST00000295641/ENST00000295641.fa | 312 ++
test/csq/ENST00000295641/ENST00000295641.fa.fai | 1 +
test/csq/ENST00000295641/ENST00000295641.gff | 54 +
test/csq/ENST00000295641/not-a-start-lost.txt | 3 +
test/csq/ENST00000295641/not-a-start-lost.txt-l | 3 +
test/csq/ENST00000295641/not-a-start-lost.vcf | 6 +
test/csq/ENST00000301246/15bp-insert.txt | 3 +
test/csq/ENST00000301246/15bp-insert.vcf | 7 +
test/csq/ENST00000301246/ENST00000301246.fa | 16 +
test/csq/ENST00000301246/ENST00000301246.fa.fai | 1 +
test/csq/ENST00000301246/ENST00000301246.gff | 23 +
test/csq/ENST00000303039/ENST00000303039.fa | 19 +
test/csq/ENST00000303039/ENST00000303039.fa.fai | 1 +
test/csq/ENST00000303039/ENST00000303039.gff | 6 +
test/csq/ENST00000303039/not-a-stop.txt | 3 +
test/csq/ENST00000303039/not-a-stop.txt-l | 3 +
test/csq/ENST00000303039/not-a-stop.vcf | 6 +
test/csq/ENST00000318249/ENST00000318249.fa | 749 +++
test/csq/ENST00000318249/ENST00000318249.fa.fai | 1 +
test/csq/ENST00000318249/ENST00000318249.gff | 34 +
test/csq/ENST00000318249/ascii-art.txt | 9 +
test/csq/ENST00000318249/start-lost.txt | 3 +
test/csq/ENST00000318249/start-lost.txt-l | 3 +
test/csq/ENST00000318249/start-lost.vcf | 6 +
test/csq/ENST00000318249/start-lost.vcf.ori | 5 +
test/csq/ENST00000318249/start-lost.vep | 14 +
test/csq/ENST00000329454/ENST00000329454.fa | 78 +
test/csq/ENST00000329454/ENST00000329454.fa.fai | 1 +
test/csq/ENST00000329454/ENST00000329454.gff | 8 +
test/csq/ENST00000329454/boundary-deletion.txt | 3 +
test/csq/ENST00000329454/boundary-deletion.txt-l | 3 +
test/csq/ENST00000329454/boundary-deletion.vcf | 6 +
test/csq/ENST00000341065/ENST00000341065.fa | 330 ++
test/csq/ENST00000341065/ENST00000341065.fa.fai | 1 +
test/csq/ENST00000341065/ENST00000341065.gff | 27 +
test/csq/ENST00000341065/ascii-art.txt | 61 +
test/csq/ENST00000341065/ascii-art.txt-l | 61 +
test/csq/ENST00000341065/frame1.txt | 3 +
test/csq/ENST00000341065/frame1.txt-l | 3 +
test/csq/ENST00000341065/frame1.vcf | 6 +
test/csq/ENST00000341065/frame2.txt | 3 +
test/csq/ENST00000341065/frame2.txt-l | 3 +
test/csq/ENST00000341065/frame2.vcf | 7 +
test/csq/ENST00000341065/frame3.txt | 3 +
test/csq/ENST00000341065/frame3.txt-l | 3 +
test/csq/ENST00000341065/frame3.vcf | 6 +
test/csq/ENST00000341065/not-a-start-lost.txt | 3 +
test/csq/ENST00000341065/not-a-start-lost.txt-l | 3 +
test/csq/ENST00000341065/not-a-start-lost.vcf | 6 +
.../csq/ENST00000341065/splice-acceptor-donor1.txt | 33 +
.../ENST00000341065/splice-acceptor-donor1.txt-l | 33 +
.../csq/ENST00000341065/splice-acceptor-donor1.vcf | 16 +
.../csq/ENST00000341065/splice-acceptor-donor2.txt | 3 +
.../ENST00000341065/splice-acceptor-donor2.txt-l | 3 +
.../csq/ENST00000341065/splice-acceptor-donor2.vcf | 6 +
.../csq/ENST00000341065/splice-acceptor-donor3.txt | 3 +
.../ENST00000341065/splice-acceptor-donor3.txt-l | 3 +
.../csq/ENST00000341065/splice-acceptor-donor3.vcf | 6 +
.../csq/ENST00000341065/splice-acceptor-donor4.txt | 3 +
.../ENST00000341065/splice-acceptor-donor4.txt-l | 3 +
.../csq/ENST00000341065/splice-acceptor-donor4.vcf | 6 +
.../csq/ENST00000341065/splice-acceptor-donor5.txt | 3 +
.../ENST00000341065/splice-acceptor-donor5.txt-l | 3 +
.../csq/ENST00000341065/splice-acceptor-donor5.vcf | 6 +
.../csq/ENST00000341065/splice-acceptor-donor6.txt | 3 +
.../ENST00000341065/splice-acceptor-donor6.txt-l | 3 +
.../csq/ENST00000341065/splice-acceptor-donor6.vcf | 6 +
.../csq/ENST00000341065/splice-acceptor-donor7.txt | 3 +
.../ENST00000341065/splice-acceptor-donor7.txt-l | 3 +
.../csq/ENST00000341065/splice-acceptor-donor7.vcf | 6 +
.../csq/ENST00000341065/splice-acceptor-donor8.txt | 3 +
.../ENST00000341065/splice-acceptor-donor8.txt-l | 3 +
.../csq/ENST00000341065/splice-acceptor-donor8.vcf | 6 +
.../csq/ENST00000341065/splice-acceptor-donor9.txt | 3 +
.../ENST00000341065/splice-acceptor-donor9.txt-l | 3 +
.../csq/ENST00000341065/splice-acceptor-donor9.vcf | 6 +
test/csq/ENST00000357367/ENST00000357367.fa | 71 +
test/csq/ENST00000357367/ENST00000357367.fa.fai | 1 +
test/csq/ENST00000357367/ENST00000357367.gff | 12 +
test/csq/ENST00000357367/stop-retained.txt | 3 +
test/csq/ENST00000357367/stop-retained.vcf | 7 +
test/csq/ENST00000368801/ENST00000368801.fa | 204 +
test/csq/ENST00000368801/ENST00000368801.fa.fai | 1 +
test/csq/ENST00000368801/ENST00000368801.gff | 10 +
test/csq/ENST00000368801/compound-lost.txt | 9 +
test/csq/ENST00000368801/compound-lost.vcf | 9 +
test/csq/ENST00000373833/ENST00000373833.fa | 557 ++
test/csq/ENST00000373833/ENST00000373833.fa.fai | 1 +
test/csq/ENST00000373833/ENST00000373833.gff | 30 +
test/csq/ENST00000373833/boundary-insertion.txt | 3 +
test/csq/ENST00000373833/boundary-insertion.txt-l | 3 +
test/csq/ENST00000373833/boundary-insertion.vcf | 6 +
test/csq/ENST00000375992/ENST00000375992.fa | 112 +
test/csq/ENST00000375992/ENST00000375992.fa.fai | 1 +
test/csq/ENST00000375992/ENST00000375992.gff | 8 +
.../incorrect-synon-del-not-start-lost.txt | 3 +
.../incorrect-synon-del-not-start-lost.vcf | 7 +
test/csq/ENST00000378322/ENST00000378322.fa | 368 ++
test/csq/ENST00000378322/ENST00000378322.fa.fai | 1 +
test/csq/ENST00000378322/ENST00000378322.gff | 26 +
test/csq/ENST00000378322/ascii-art.txt | 9 +
test/csq/ENST00000378322/ascii-art.txt-l | 9 +
test/csq/ENST00000378322/end-overlap-tscript.txt | 9 +
test/csq/ENST00000378322/end-overlap-tscript.txt-l | 9 +
test/csq/ENST00000378322/end-overlap-tscript.vcf | 8 +
test/csq/ENST00000381157/ENST00000381157.fa | 903 +++
test/csq/ENST00000381157/ENST00000381157.fa.fai | 1 +
test/csq/ENST00000381157/ENST00000381157.gff | 14 +
test/csq/ENST00000381157/haploid-diploid.txt | 9 +
test/csq/ENST00000381157/haploid-diploid.vcf | 11 +
test/csq/ENST00000382647/ENST00000382647.fa | 52 +
test/csq/ENST00000382647/ENST00000382647.fa.fai | 1 +
test/csq/ENST00000382647/ENST00000382647.gff | 8 +
.../ENST00000382647/synon-splice-region-insert.txt | 3 +
.../ENST00000382647/synon-splice-region-insert.vcf | 7 +
test/csq/ENST00000390520/ENST00000390520.fa | 3 +
test/csq/ENST00000390520/ENST00000390520.fa.fai | 1 +
test/csq/ENST00000390520/ENST00000390520.gff | 4 +
test/csq/ENST00000390520/deletion-overlap.txt | 3 +
test/csq/ENST00000390520/deletion-overlap.vcf | 7 +
test/csq/ENST00000409523/ENST00000409523.fa | 1079 ++++
test/csq/ENST00000409523/ENST00000409523.fa.fai | 1 +
test/csq/ENST00000409523/ENST00000409523.gff | 16 +
test/csq/ENST00000409523/ascii-art.txt | 30 +
test/csq/ENST00000409523/long-overlapping-del.txt | 6 +
test/csq/ENST00000409523/long-overlapping-del.vcf | 8 +
test/csq/ENST00000410009/ENST00000410009.fa | 96 +
test/csq/ENST00000410009/ENST00000410009.fa.fai | 1 +
test/csq/ENST00000410009/ENST00000410009.gff | 16 +
test/csq/ENST00000410009/ascii-art.txt | 7 +
test/csq/ENST00000410009/frameshift.txt | 3 +
test/csq/ENST00000410009/frameshift.vcf | 7 +
test/csq/ENST00000413103/ENST00000413103.fa | 29 +
test/csq/ENST00000413103/ENST00000413103.fa.fai | 1 +
test/csq/ENST00000413103/ENST00000413103.gff | 4 +
test/csq/ENST00000413103/long-deletion.txt | 3 +
test/csq/ENST00000413103/long-deletion.vcf | 7 +
test/csq/ENST00000420670/ENST00000420670.fa | 2291 ++++++++
test/csq/ENST00000420670/ENST00000420670.fa.fai | 1 +
test/csq/ENST00000420670/ENST00000420670.gff | 11 +
test/csq/ENST00000420670/start-stop-lost.txt | 3 +
test/csq/ENST00000420670/start-stop-lost.vcf | 7 +
test/csq/ENST00000423372/ENST00000423372.fa | 76 +
test/csq/ENST00000423372/ENST00000423372.fa.fai | 1 +
test/csq/ENST00000423372/ENST00000423372.gff | 8 +
test/csq/ENST00000423372/insert3.txt | 6 +
test/csq/ENST00000423372/insert3.txt-l | 6 +
test/csq/ENST00000423372/insert3.vcf | 7 +
test/csq/ENST00000423372/snps.txt | 117 +
test/csq/ENST00000423372/snps.txt-l | 117 +
test/csq/ENST00000423372/snps.vcf | 45 +
test/csq/ENST00000436063/ENST00000436063.fa | 204 +
test/csq/ENST00000436063/ENST00000436063.fa.fai | 1 +
test/csq/ENST00000436063/ENST00000436063.gff | 18 +
test/csq/ENST00000436063/insert-before-utr.txt | 3 +
test/csq/ENST00000436063/insert-before-utr.vcf | 7 +
test/csq/ENST00000448695/ENST00000448695.fa | 2528 +++++++++
test/csq/ENST00000448695/ENST00000448695.fa.fai | 1 +
test/csq/ENST00000448695/ENST00000448695.gff | 55 +
test/csq/ENST00000448695/syn-and-splice-reg.txt | 3 +
test/csq/ENST00000448695/syn-and-splice-reg.vcf | 7 +
test/csq/ENST00000479739/ENST00000479739.fa | 813 +++
test/csq/ENST00000479739/ENST00000479739.fa.fai | 1 +
test/csq/ENST00000479739/ENST00000479739.gff | 26 +
test/csq/ENST00000479739/short-cds-start-lost.txt | 3 +
.../csq/ENST00000479739/short-cds-start-lost.txt-l | 3 +
test/csq/ENST00000479739/short-cds-start-lost.vcf | 6 +
test/csq/ENST00000519442/ENST00000519442.fa | 766 +++
test/csq/ENST00000519442/ENST00000519442.fa.fai | 1 +
test/csq/ENST00000519442/ENST00000519442.gff | 16 +
.../ENST00000519442/synon-splice-region-del.txt | 3 +
.../ENST00000519442/synon-splice-region-del.vcf | 7 +
test/csq/ENST00000520795/ENST00000520795.fa | 4550 ++++++++++++++++
test/csq/ENST00000520795/ENST00000520795.fa.fai | 1 +
test/csq/ENST00000520795/ENST00000520795.gff | 8 +
test/csq/ENST00000520795/ascii-art.txt | 9 +
test/csq/ENST00000520795/ascii-art.txt-l | 9 +
test/csq/ENST00000520795/long-inside-del.txt | 3 +
test/csq/ENST00000520795/long-inside-del.txt-l | 3 +
test/csq/ENST00000520795/long-inside-del.vcf | 6 +
test/csq/ENST00000520868/ENST00000520868.fa | 621 +++
test/csq/ENST00000520868/ENST00000520868.fa.fai | 1 +
test/csq/ENST00000520868/ENST00000520868.gff | 15 +
test/csq/ENST00000520868/ascii-art.txt | 6 +
test/csq/ENST00000520868/long-deletion.txt | 3 +
test/csq/ENST00000520868/long-deletion.vcf | 7 +
test/csq/ENST00000528237/ENST00000528237.fa | 993 ++++
test/csq/ENST00000528237/ENST00000528237.fa.fai | 1 +
test/csq/ENST00000528237/ENST00000528237.gff | 17 +
.../retained-stop-incomplete-cds.txt | 3 +
.../retained-stop-incomplete-cds.vcf | 7 +
test/csq/ENST00000536784/ENST00000536784.fa | 259 +
test/csq/ENST00000536784/ENST00000536784.fa.fai | 1 +
test/csq/ENST00000536784/ENST00000536784.gff | 9 +
test/csq/ENST00000536784/not-a-start-lost.txt | 3 +
test/csq/ENST00000536784/not-a-start-lost.txt-l | 3 +
test/csq/ENST00000536784/not-a-start-lost.vcf | 6 +
test/csq/ENST00000542803/ENST00000542803.fa | 5726 ++++++++++++++++++++
test/csq/ENST00000542803/ENST00000542803.fa.fai | 1 +
test/csq/ENST00000542803/ENST00000542803.gff | 22 +
test/csq/ENST00000542803/splice-region.txt | 3 +
test/csq/ENST00000542803/splice-region.txt-l | 3 +
test/csq/ENST00000542803/splice-region.vcf | 6 +
test/csq/ENST00000543077/ENST00000543077.fa | 292 +
test/csq/ENST00000543077/ENST00000543077.fa.fai | 1 +
test/csq/ENST00000543077/ENST00000543077.gff | 7 +
test/csq/ENST00000543077/not-a-start-lost.txt | 3 +
test/csq/ENST00000543077/not-a-start-lost.txt-l | 3 +
test/csq/ENST00000543077/not-a-start-lost.vcf | 6 +
test/csq/ENST00000545279/ENST00000545279.fa | 934 ++++
test/csq/ENST00000545279/ENST00000545279.fa.fai | 1 +
test/csq/ENST00000545279/ENST00000545279.gff | 22 +
test/csq/ENST00000545279/splice-region-insert.txt | 3 +
test/csq/ENST00000545279/splice-region-insert.vcf | 7 +
test/csq/ENST00000557788/ENST00000557788.fa | 12 +
test/csq/ENST00000557788/ENST00000557788.fa.fai | 1 +
test/csq/ENST00000557788/ENST00000557788.gff | 6 +
test/csq/ENST00000557788/ascii-art.txt | 6 +
test/csq/ENST00000557788/long-overlap-del.txt | 3 +
test/csq/ENST00000557788/long-overlap-del.vcf | 7 +
test/csq/ENST00000573314/ENST00000573314.fa | 544 ++
test/csq/ENST00000573314/ENST00000573314.fa.fai | 1 +
test/csq/ENST00000573314/ENST00000573314.gff | 28 +
test/csq/ENST00000573314/ascii-art.txt | 16 +
test/csq/ENST00000573314/ascii-art.txt-l | 16 +
.../incorrect-insertion-overlap.txt | 3 +
.../incorrect-insertion-overlap.txt-l | 3 +
.../incorrect-insertion-overlap.vcf | 6 +
test/csq/ENST00000593942/ENST00000593942.fa | 345 ++
test/csq/ENST00000593942/ENST00000593942.fa.fai | 1 +
test/csq/ENST00000593942/ENST00000593942.gff | 18 +
test/csq/ENST00000593942/last-codon-deletion.txt | 3 +
test/csq/ENST00000593942/last-codon-deletion.vcf | 7 +
test/csq/ENST00000624631/ENST00000624631.fa | 25 +
test/csq/ENST00000624631/ENST00000624631.fa.fai | 1 +
test/csq/ENST00000624631/ENST00000624631.gff | 8 +
test/csq/ENST00000624631/ambiguous.txt | 3 +
test/csq/ENST00000624631/ambiguous.vcf | 7 +
test/csq/ENST00000624631/ascii-art.txt | 11 +
test/csq/ENST00000624631/segfault.txt.new | 3 +
test/csq/make-csq-test | 276 +
test/csq/sort-csq | 62 +
test/fill-tags-hemi.1.out | 19 +
test/fill-tags-hemi.2.out | 19 +
test/{stats.a.vcf => fill-tags-hemi.vcf} | 9 +-
test/fill-tags.2.out | 27 +-
test/{fill-tags.2.out => fill-tags.3.out} | 34 +-
test/fill-tags.3.smpl | 3 +
test/filter-missing-floats.vcf | 42 +
test/fixref.1.out | 31 +
test/fixref.vcf | 31 +
test/guess-ploidy.GL.out | 4 +
test/guess-ploidy.PL.out | 4 +
test/gvcf.merge.1.out | 30 +
test/gvcf.merge.1.vcf | 26 +
test/gvcf.merge.2.vcf | 26 +
test/gvcf.merge.3.vcf | 26 +
test/isec.ab.any.out | 2 +
test/isec.ab.both.out | 1 +
test/large_chrom_tbi_limit.20.1.536870912.out | 3 -
test/large_chrom_tbi_limit.vcf | 20 -
test/mendelian.1.out | 9 +
test/mendelian.2.out | 8 +
test/{stats.a.vcf => mendelian.3.out} | 7 +-
test/mendelian.vcf | 8 +
test/merge.2.both.out | 4 +-
test/merge.2.none.out | 6 +-
test/merge.5.a.vcf | 8 +
test/merge.5.b.vcf | 7 +
test/merge.5.out | 9 +
test/{merge.abc.out => merge.abc.2.out} | 11 +-
test/{merge.abc.out => merge.abc.3.out} | 31 +-
test/merge.abc.out | 9 +-
test/merge.gvcf.2.a.vcf | 33 +
test/merge.gvcf.2.b.vcf | 33 +
test/merge.gvcf.2.c.vcf | 12 +
test/merge.gvcf.2.out | 53 +
test/mpileup.2.samples | 3 +
test/{mpileup.X.out => mpileup.X.2.out} | 22 +-
test/mpileup.X.out | 12 +-
test/mpileup.c.X.2.out | 43 +
test/mpileup.cAls.out | 14 +-
test/mpileup/mpileup.1.bam | Bin 0 -> 67789 bytes
test/mpileup/mpileup.1.bam.bai | Bin 0 -> 96 bytes
test/mpileup/mpileup.1.cram | Bin 0 -> 49113 bytes
test/mpileup/mpileup.1.cram.crai | Bin 0 -> 42 bytes
test/mpileup/mpileup.1.out | 70 +
test/mpileup/mpileup.1.sam | 1016 ++++
test/mpileup/mpileup.10.out | 70 +
test/mpileup/mpileup.11.out | 4021 ++++++++++++++
test/mpileup/mpileup.2.bam | Bin 0 -> 27928 bytes
test/mpileup/mpileup.2.bam.bai | Bin 0 -> 96 bytes
test/mpileup/mpileup.2.cram | Bin 0 -> 20072 bytes
test/mpileup/mpileup.2.cram.crai | Bin 0 -> 45 bytes
test/mpileup/mpileup.2.out | 523 ++
test/mpileup/mpileup.2.sam | 248 +
test/mpileup/mpileup.3.bam | Bin 0 -> 27569 bytes
test/mpileup/mpileup.3.bam.bai | Bin 0 -> 96 bytes
test/mpileup/mpileup.3.cram | Bin 0 -> 19643 bytes
test/mpileup/mpileup.3.cram.crai | Bin 0 -> 43 bytes
test/mpileup/mpileup.3.out | 30 +
test/mpileup/mpileup.3.sam | 250 +
test/mpileup/mpileup.4.bam | Bin 0 -> 26690 bytes
test/mpileup/mpileup.4.cram | Bin 0 -> 28165 bytes
test/mpileup/mpileup.4.out | 527 ++
test/mpileup/mpileup.4.sam | 238 +
test/mpileup/mpileup.5.out | 529 ++
test/mpileup/mpileup.6.out | 65 +
test/mpileup/mpileup.7.out | 70 +
test/mpileup/mpileup.8.out | 70 +
test/mpileup/mpileup.9.out | 70 +
test/mpileup/mpileup.ref.fa | 71 +
test/mpileup/mpileup.ref.fa.fai | 1 +
test/mplp.10.samples | 5 +
test/mplp.11.rgs | 1 +
test/mplp.9.samples | 2 +
test/mplp.samples | 2 +
test/norm.out | 1 +
test/norm.vcf | 2 +
test/query.24.out | 3 +
test/query.25.out | 13 +
test/query.26.out | 1 +
test/query.27.out | 2 +
test/query.28.out | 4 +
test/query.29.out | 3 +
test/query.30.out | 19 +
test/query.31.out | 16 +
test/query.32.out | 3 +
test/query.33.out | 4 +
test/query.filter-type.vcf | 21 +
test/query.filter.2.vcf | 14 +
test/ref.out | 30 +
test/ref.vcf | 30 +
test/{merge.2.both.out => setGT.1.out} | 29 +-
test/{merge.2.both.out => setGT.vcf} | 29 +-
test/{stats.chk => stats.B.chk} | 46 +-
test/stats.a.vcf | 1 +
test/stats.b.vcf | 1 +
test/stats.chk | 40 +-
test/test-rbuf.c | 6 +-
test/test-regidx.c | 374 ++
test/test.pl | 250 +-
test/trio.out | 7 +
test/trio.ped | 6 +
test/trio.vcf | 16 +
test/view.GP.vcf | 42 +
test/view.GT.vcf | 42 +
test/{fill-tags.2.out => view.GTsubset.NA1.out} | 23 +-
test/{fill-tags.2.out => view.GTsubset.NA1NA2.out} | 26 +-
test/view.GTsubset.NA1NA2NA3.out | 36 +
test/view.vectors.2.vcf | 25 +
test/view.vectors.C.out | 28 +
tsv2vcf.c | 1 +
vcfannotate.c | 744 +--
vcfcall.c | 44 +-
vcfcnv.c | 46 +-
vcfconcat.c | 164 +-
vcfconvert.c | 120 +-
vcffilter.c | 3 +-
vcfgtcheck.c | 298 +-
vcfindex.c | 115 +-
vcfisec.c | 2 +-
vcfmerge.c | 1075 ++--
vcfnorm.c | 82 +-
vcfplugin.c | 56 +-
vcfroh.c | 961 +++-
vcfstats.c | 429 +-
vcfview.c | 50 +-
484 files changed, 62048 insertions(+), 3674 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bcftools.git
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