[med-svn] [bcftools] branch upstream updated (c7f7f8b -> 0fb5584)
Andreas Tille
tille at debian.org
Sun Jun 18 20:00:13 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository bcftools.
from c7f7f8b Imported Upstream version 1.3.1
new 0fb5584 New upstream version 1.4.1
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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 ++
version.c => bam_sample.h | 59 +-
bcftools.h | 1 +
bin.c | 104 +
peakfit.h => bin.h | 50 +-
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/{GTisec.mk => 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/{annotate2.vcf => annotate11.out} | 7 +-
test/{annotate2.vcf => annotate12.out} | 9 +-
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.b.vcf => fill-tags-hemi.vcf} | 9 +-
test/fill-tags.2.out | 27 +-
test/{view.vcf => fill-tags.3.out} | 31 +-
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.b.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.out => mpileup.c.X.2.out} | 10 +-
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.23.out => query.24.out} | 2 +-
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.vcf => query.filter-type.vcf} | 9 +-
test/query.filter.2.vcf | 14 +
test/ref.out | 30 +
test/ref.vcf | 30 +
test/{plugin1.vcf => setGT.1.out} | 13 +-
test/{plugin1.vcf => setGT.vcf} | 9 +-
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/{view.10.out => view.GTsubset.NA1.out} | 4 +-
test/{view.6.out => view.GTsubset.NA1NA2.out} | 6 +-
test/{view.10.out => view.GTsubset.NA1NA2NA3.out} | 4 +-
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, 61842 insertions(+), 3696 deletions(-)
create mode 100644 NEWS
create mode 100644 bam2bcf.c
create mode 100644 bam2bcf.h
create mode 100644 bam2bcf_indel.c
create mode 100644 bam_sample.c
copy version.c => bam_sample.h (51%)
create mode 100644 bin.c
copy peakfit.h => bin.h (53%)
create mode 100644 csq.c
create mode 100644 hclust.c
create mode 100644 hclust.h
create mode 100644 kheap.h
rename {plugins => misc}/color-chrs.pl (100%)
create mode 100755 misc/guess-ploidy.py
create mode 100755 misc/plot-roh.py
rename plot-vcfstats => misc/plot-vcfstats (86%)
create mode 100755 misc/run-roh.pl
rename vcfutils.pl => misc/vcfutils.pl (100%)
create mode 100644 mpileup.c
create mode 100644 mw.h
create mode 100644 plugins/GTsubset.c
copy plugins/{GTisec.mk => GTsubset.mk} (62%)
create mode 100644 plugins/ad-bias.c
create mode 100644 plugins/ad-bias.mk
create mode 100644 plugins/af-dist.c
create mode 100644 plugins/af-dist.mk
create mode 100644 plugins/check-sparsity.c
create mode 100644 plugins/fill-from-fasta.c
create mode 100644 plugins/fill-from-fasta.mk
create mode 100644 plugins/fixref.c
create mode 100644 plugins/guess-ploidy.c
create mode 100644 plugins/isecGT.c
create mode 100644 plugins/setGT.mk
create mode 100644 plugins/trio-switch-rate.c
delete mode 100644 plugins/vcf2sex.c
delete mode 100644 plugins/vcf2sex.mk
create mode 100644 regidx.c
create mode 100644 regidx.h
create mode 100644 smpl_ilist.c
create mode 100644 smpl_ilist.h
create mode 100644 test/aa.fa
create mode 100644 test/aa.fa.fai
create mode 100644 test/aa.hdr
create mode 100644 test/aa.out
create mode 100644 test/aa.vcf
create mode 100644 test/ad-bias.out
create mode 100644 test/ad-bias.samples
create mode 100644 test/ad-bias.vcf
create mode 100644 test/af-dist.out
create mode 100644 test/af-dist.vcf
copy test/{annotate2.vcf => annotate11.out} (82%)
copy test/{annotate2.vcf => annotate12.out} (63%)
create mode 100644 test/annotate13.out
create mode 100644 test/annots11.tab
create mode 100644 test/csq.1.out
create mode 100644 test/csq.fa
create mode 100644 test/csq.fa.fai
create mode 100644 test/csq.gff3
create mode 100644 test/csq.vcf
create mode 100644 test/csq/ENSG00000173376/ENSG00000173376.fa
create mode 100644 test/csq/ENSG00000173376/ENSG00000173376.fa.fai
create mode 100644 test/csq/ENSG00000173376/ENSG00000173376.gff
create mode 100644 test/csq/ENSG00000173376/synon.txt
create mode 100644 test/csq/ENSG00000173376/synon.vcf
create mode 100644 test/csq/ENST00000218032/ENST00000218032.fa
create mode 100644 test/csq/ENST00000218032/ENST00000218032.fa.fai
create mode 100644 test/csq/ENST00000218032/ENST00000218032.gff
create mode 100644 test/csq/ENST00000218032/start-lost.txt
create mode 100644 test/csq/ENST00000218032/start-lost.txt-l
create mode 100644 test/csq/ENST00000218032/start-lost.vcf
create mode 100644 test/csq/ENST00000227471/ENST00000227471.fa
create mode 100644 test/csq/ENST00000227471/ENST00000227471.fa.fai
create mode 100644 test/csq/ENST00000227471/ENST00000227471.gff
create mode 100644 test/csq/ENST00000227471/insert-splice-vs-frameshift.txt
create mode 100644 test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf
create mode 100644 test/csq/ENST00000256452/ENST00000256452.fa
create mode 100644 test/csq/ENST00000256452/ENST00000256452.fa.fai
create mode 100644 test/csq/ENST00000256452/ENST00000256452.gff
create mode 100644 test/csq/ENST00000256452/intron.txt
create mode 100644 test/csq/ENST00000256452/intron.vcf
create mode 100644 test/csq/ENST00000294661/ENST00000294661.fa
create mode 100644 test/csq/ENST00000294661/ENST00000294661.fa.fai
create mode 100644 test/csq/ENST00000294661/ENST00000294661.gff
create mode 100644 test/csq/ENST00000294661/non-coding-boundary.txt
create mode 100644 test/csq/ENST00000294661/non-coding-boundary.txt-l
create mode 100644 test/csq/ENST00000294661/non-coding-boundary.vcf
create mode 100644 test/csq/ENST00000295641/ENST00000295641.fa
create mode 100644 test/csq/ENST00000295641/ENST00000295641.fa.fai
create mode 100644 test/csq/ENST00000295641/ENST00000295641.gff
create mode 100644 test/csq/ENST00000295641/not-a-start-lost.txt
create mode 100644 test/csq/ENST00000295641/not-a-start-lost.txt-l
create mode 100644 test/csq/ENST00000295641/not-a-start-lost.vcf
create mode 100644 test/csq/ENST00000301246/15bp-insert.txt
create mode 100644 test/csq/ENST00000301246/15bp-insert.vcf
create mode 100644 test/csq/ENST00000301246/ENST00000301246.fa
create mode 100644 test/csq/ENST00000301246/ENST00000301246.fa.fai
create mode 100644 test/csq/ENST00000301246/ENST00000301246.gff
create mode 100644 test/csq/ENST00000303039/ENST00000303039.fa
create mode 100644 test/csq/ENST00000303039/ENST00000303039.fa.fai
create mode 100644 test/csq/ENST00000303039/ENST00000303039.gff
create mode 100644 test/csq/ENST00000303039/not-a-stop.txt
create mode 100644 test/csq/ENST00000303039/not-a-stop.txt-l
create mode 100644 test/csq/ENST00000303039/not-a-stop.vcf
create mode 100644 test/csq/ENST00000318249/ENST00000318249.fa
create mode 100644 test/csq/ENST00000318249/ENST00000318249.fa.fai
create mode 100644 test/csq/ENST00000318249/ENST00000318249.gff
create mode 100644 test/csq/ENST00000318249/ascii-art.txt
create mode 100644 test/csq/ENST00000318249/start-lost.txt
create mode 100644 test/csq/ENST00000318249/start-lost.txt-l
create mode 100644 test/csq/ENST00000318249/start-lost.vcf
create mode 100644 test/csq/ENST00000318249/start-lost.vcf.ori
create mode 100644 test/csq/ENST00000318249/start-lost.vep
create mode 100644 test/csq/ENST00000329454/ENST00000329454.fa
create mode 100644 test/csq/ENST00000329454/ENST00000329454.fa.fai
create mode 100644 test/csq/ENST00000329454/ENST00000329454.gff
create mode 100644 test/csq/ENST00000329454/boundary-deletion.txt
create mode 100644 test/csq/ENST00000329454/boundary-deletion.txt-l
create mode 100644 test/csq/ENST00000329454/boundary-deletion.vcf
create mode 100644 test/csq/ENST00000341065/ENST00000341065.fa
create mode 100644 test/csq/ENST00000341065/ENST00000341065.fa.fai
create mode 100644 test/csq/ENST00000341065/ENST00000341065.gff
create mode 100644 test/csq/ENST00000341065/ascii-art.txt
create mode 100644 test/csq/ENST00000341065/ascii-art.txt-l
create mode 100644 test/csq/ENST00000341065/frame1.txt
create mode 100644 test/csq/ENST00000341065/frame1.txt-l
create mode 100644 test/csq/ENST00000341065/frame1.vcf
create mode 100644 test/csq/ENST00000341065/frame2.txt
create mode 100644 test/csq/ENST00000341065/frame2.txt-l
create mode 100644 test/csq/ENST00000341065/frame2.vcf
create mode 100644 test/csq/ENST00000341065/frame3.txt
create mode 100644 test/csq/ENST00000341065/frame3.txt-l
create mode 100644 test/csq/ENST00000341065/frame3.vcf
create mode 100644 test/csq/ENST00000341065/not-a-start-lost.txt
create mode 100644 test/csq/ENST00000341065/not-a-start-lost.txt-l
create mode 100644 test/csq/ENST00000341065/not-a-start-lost.vcf
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor1.txt
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor1.txt-l
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor1.vcf
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor2.txt
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor2.txt-l
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor2.vcf
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor3.txt
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor3.txt-l
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor3.vcf
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor4.txt
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor4.txt-l
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor4.vcf
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor5.txt
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor5.txt-l
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor5.vcf
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor6.txt
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor6.txt-l
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor6.vcf
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor7.txt
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor7.txt-l
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor7.vcf
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor8.txt
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor8.txt-l
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor8.vcf
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor9.txt
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor9.txt-l
create mode 100644 test/csq/ENST00000341065/splice-acceptor-donor9.vcf
create mode 100644 test/csq/ENST00000357367/ENST00000357367.fa
create mode 100644 test/csq/ENST00000357367/ENST00000357367.fa.fai
create mode 100644 test/csq/ENST00000357367/ENST00000357367.gff
create mode 100644 test/csq/ENST00000357367/stop-retained.txt
create mode 100644 test/csq/ENST00000357367/stop-retained.vcf
create mode 100644 test/csq/ENST00000368801/ENST00000368801.fa
create mode 100644 test/csq/ENST00000368801/ENST00000368801.fa.fai
create mode 100644 test/csq/ENST00000368801/ENST00000368801.gff
create mode 100644 test/csq/ENST00000368801/compound-lost.txt
create mode 100644 test/csq/ENST00000368801/compound-lost.vcf
create mode 100644 test/csq/ENST00000373833/ENST00000373833.fa
create mode 100644 test/csq/ENST00000373833/ENST00000373833.fa.fai
create mode 100644 test/csq/ENST00000373833/ENST00000373833.gff
create mode 100644 test/csq/ENST00000373833/boundary-insertion.txt
create mode 100644 test/csq/ENST00000373833/boundary-insertion.txt-l
create mode 100644 test/csq/ENST00000373833/boundary-insertion.vcf
create mode 100644 test/csq/ENST00000375992/ENST00000375992.fa
create mode 100644 test/csq/ENST00000375992/ENST00000375992.fa.fai
create mode 100644 test/csq/ENST00000375992/ENST00000375992.gff
create mode 100644 test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.txt
create mode 100644 test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf
create mode 100644 test/csq/ENST00000378322/ENST00000378322.fa
create mode 100644 test/csq/ENST00000378322/ENST00000378322.fa.fai
create mode 100644 test/csq/ENST00000378322/ENST00000378322.gff
create mode 100644 test/csq/ENST00000378322/ascii-art.txt
create mode 100644 test/csq/ENST00000378322/ascii-art.txt-l
create mode 100644 test/csq/ENST00000378322/end-overlap-tscript.txt
create mode 100644 test/csq/ENST00000378322/end-overlap-tscript.txt-l
create mode 100644 test/csq/ENST00000378322/end-overlap-tscript.vcf
create mode 100644 test/csq/ENST00000381157/ENST00000381157.fa
create mode 100644 test/csq/ENST00000381157/ENST00000381157.fa.fai
create mode 100644 test/csq/ENST00000381157/ENST00000381157.gff
create mode 100644 test/csq/ENST00000381157/haploid-diploid.txt
create mode 100644 test/csq/ENST00000381157/haploid-diploid.vcf
create mode 100644 test/csq/ENST00000382647/ENST00000382647.fa
create mode 100644 test/csq/ENST00000382647/ENST00000382647.fa.fai
create mode 100644 test/csq/ENST00000382647/ENST00000382647.gff
create mode 100644 test/csq/ENST00000382647/synon-splice-region-insert.txt
create mode 100644 test/csq/ENST00000382647/synon-splice-region-insert.vcf
create mode 100644 test/csq/ENST00000390520/ENST00000390520.fa
create mode 100644 test/csq/ENST00000390520/ENST00000390520.fa.fai
create mode 100644 test/csq/ENST00000390520/ENST00000390520.gff
create mode 100644 test/csq/ENST00000390520/deletion-overlap.txt
create mode 100644 test/csq/ENST00000390520/deletion-overlap.vcf
create mode 100644 test/csq/ENST00000409523/ENST00000409523.fa
create mode 100644 test/csq/ENST00000409523/ENST00000409523.fa.fai
create mode 100644 test/csq/ENST00000409523/ENST00000409523.gff
create mode 100644 test/csq/ENST00000409523/ascii-art.txt
create mode 100644 test/csq/ENST00000409523/long-overlapping-del.txt
create mode 100644 test/csq/ENST00000409523/long-overlapping-del.vcf
create mode 100644 test/csq/ENST00000410009/ENST00000410009.fa
create mode 100644 test/csq/ENST00000410009/ENST00000410009.fa.fai
create mode 100644 test/csq/ENST00000410009/ENST00000410009.gff
create mode 100644 test/csq/ENST00000410009/ascii-art.txt
create mode 100644 test/csq/ENST00000410009/frameshift.txt
create mode 100644 test/csq/ENST00000410009/frameshift.vcf
create mode 100644 test/csq/ENST00000413103/ENST00000413103.fa
create mode 100644 test/csq/ENST00000413103/ENST00000413103.fa.fai
create mode 100644 test/csq/ENST00000413103/ENST00000413103.gff
create mode 100644 test/csq/ENST00000413103/long-deletion.txt
create mode 100644 test/csq/ENST00000413103/long-deletion.vcf
create mode 100644 test/csq/ENST00000420670/ENST00000420670.fa
create mode 100644 test/csq/ENST00000420670/ENST00000420670.fa.fai
create mode 100644 test/csq/ENST00000420670/ENST00000420670.gff
create mode 100644 test/csq/ENST00000420670/start-stop-lost.txt
create mode 100644 test/csq/ENST00000420670/start-stop-lost.vcf
create mode 100644 test/csq/ENST00000423372/ENST00000423372.fa
create mode 100644 test/csq/ENST00000423372/ENST00000423372.fa.fai
create mode 100644 test/csq/ENST00000423372/ENST00000423372.gff
create mode 100644 test/csq/ENST00000423372/insert3.txt
create mode 100644 test/csq/ENST00000423372/insert3.txt-l
create mode 100644 test/csq/ENST00000423372/insert3.vcf
create mode 100644 test/csq/ENST00000423372/snps.txt
create mode 100644 test/csq/ENST00000423372/snps.txt-l
create mode 100644 test/csq/ENST00000423372/snps.vcf
create mode 100644 test/csq/ENST00000436063/ENST00000436063.fa
create mode 100644 test/csq/ENST00000436063/ENST00000436063.fa.fai
create mode 100644 test/csq/ENST00000436063/ENST00000436063.gff
create mode 100644 test/csq/ENST00000436063/insert-before-utr.txt
create mode 100644 test/csq/ENST00000436063/insert-before-utr.vcf
create mode 100644 test/csq/ENST00000448695/ENST00000448695.fa
create mode 100644 test/csq/ENST00000448695/ENST00000448695.fa.fai
create mode 100644 test/csq/ENST00000448695/ENST00000448695.gff
create mode 100644 test/csq/ENST00000448695/syn-and-splice-reg.txt
create mode 100644 test/csq/ENST00000448695/syn-and-splice-reg.vcf
create mode 100644 test/csq/ENST00000479739/ENST00000479739.fa
create mode 100644 test/csq/ENST00000479739/ENST00000479739.fa.fai
create mode 100644 test/csq/ENST00000479739/ENST00000479739.gff
create mode 100644 test/csq/ENST00000479739/short-cds-start-lost.txt
create mode 100644 test/csq/ENST00000479739/short-cds-start-lost.txt-l
create mode 100644 test/csq/ENST00000479739/short-cds-start-lost.vcf
create mode 100644 test/csq/ENST00000519442/ENST00000519442.fa
create mode 100644 test/csq/ENST00000519442/ENST00000519442.fa.fai
create mode 100644 test/csq/ENST00000519442/ENST00000519442.gff
create mode 100644 test/csq/ENST00000519442/synon-splice-region-del.txt
create mode 100644 test/csq/ENST00000519442/synon-splice-region-del.vcf
create mode 100644 test/csq/ENST00000520795/ENST00000520795.fa
create mode 100644 test/csq/ENST00000520795/ENST00000520795.fa.fai
create mode 100644 test/csq/ENST00000520795/ENST00000520795.gff
create mode 100644 test/csq/ENST00000520795/ascii-art.txt
create mode 100644 test/csq/ENST00000520795/ascii-art.txt-l
create mode 100644 test/csq/ENST00000520795/long-inside-del.txt
create mode 100644 test/csq/ENST00000520795/long-inside-del.txt-l
create mode 100644 test/csq/ENST00000520795/long-inside-del.vcf
create mode 100644 test/csq/ENST00000520868/ENST00000520868.fa
create mode 100644 test/csq/ENST00000520868/ENST00000520868.fa.fai
create mode 100644 test/csq/ENST00000520868/ENST00000520868.gff
create mode 100644 test/csq/ENST00000520868/ascii-art.txt
create mode 100644 test/csq/ENST00000520868/long-deletion.txt
create mode 100644 test/csq/ENST00000520868/long-deletion.vcf
create mode 100644 test/csq/ENST00000528237/ENST00000528237.fa
create mode 100644 test/csq/ENST00000528237/ENST00000528237.fa.fai
create mode 100644 test/csq/ENST00000528237/ENST00000528237.gff
create mode 100644 test/csq/ENST00000528237/retained-stop-incomplete-cds.txt
create mode 100644 test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf
create mode 100644 test/csq/ENST00000536784/ENST00000536784.fa
create mode 100644 test/csq/ENST00000536784/ENST00000536784.fa.fai
create mode 100644 test/csq/ENST00000536784/ENST00000536784.gff
create mode 100644 test/csq/ENST00000536784/not-a-start-lost.txt
create mode 100644 test/csq/ENST00000536784/not-a-start-lost.txt-l
create mode 100644 test/csq/ENST00000536784/not-a-start-lost.vcf
create mode 100644 test/csq/ENST00000542803/ENST00000542803.fa
create mode 100644 test/csq/ENST00000542803/ENST00000542803.fa.fai
create mode 100644 test/csq/ENST00000542803/ENST00000542803.gff
create mode 100644 test/csq/ENST00000542803/splice-region.txt
create mode 100644 test/csq/ENST00000542803/splice-region.txt-l
create mode 100644 test/csq/ENST00000542803/splice-region.vcf
create mode 100644 test/csq/ENST00000543077/ENST00000543077.fa
create mode 100644 test/csq/ENST00000543077/ENST00000543077.fa.fai
create mode 100644 test/csq/ENST00000543077/ENST00000543077.gff
create mode 100644 test/csq/ENST00000543077/not-a-start-lost.txt
create mode 100644 test/csq/ENST00000543077/not-a-start-lost.txt-l
create mode 100644 test/csq/ENST00000543077/not-a-start-lost.vcf
create mode 100644 test/csq/ENST00000545279/ENST00000545279.fa
create mode 100644 test/csq/ENST00000545279/ENST00000545279.fa.fai
create mode 100644 test/csq/ENST00000545279/ENST00000545279.gff
create mode 100644 test/csq/ENST00000545279/splice-region-insert.txt
create mode 100644 test/csq/ENST00000545279/splice-region-insert.vcf
create mode 100644 test/csq/ENST00000557788/ENST00000557788.fa
create mode 100644 test/csq/ENST00000557788/ENST00000557788.fa.fai
create mode 100644 test/csq/ENST00000557788/ENST00000557788.gff
create mode 100644 test/csq/ENST00000557788/ascii-art.txt
create mode 100644 test/csq/ENST00000557788/long-overlap-del.txt
create mode 100644 test/csq/ENST00000557788/long-overlap-del.vcf
create mode 100644 test/csq/ENST00000573314/ENST00000573314.fa
create mode 100644 test/csq/ENST00000573314/ENST00000573314.fa.fai
create mode 100644 test/csq/ENST00000573314/ENST00000573314.gff
create mode 100644 test/csq/ENST00000573314/ascii-art.txt
create mode 100644 test/csq/ENST00000573314/ascii-art.txt-l
create mode 100644 test/csq/ENST00000573314/incorrect-insertion-overlap.txt
create mode 100644 test/csq/ENST00000573314/incorrect-insertion-overlap.txt-l
create mode 100644 test/csq/ENST00000573314/incorrect-insertion-overlap.vcf
create mode 100644 test/csq/ENST00000593942/ENST00000593942.fa
create mode 100644 test/csq/ENST00000593942/ENST00000593942.fa.fai
create mode 100644 test/csq/ENST00000593942/ENST00000593942.gff
create mode 100644 test/csq/ENST00000593942/last-codon-deletion.txt
create mode 100644 test/csq/ENST00000593942/last-codon-deletion.vcf
create mode 100644 test/csq/ENST00000624631/ENST00000624631.fa
create mode 100644 test/csq/ENST00000624631/ENST00000624631.fa.fai
create mode 100644 test/csq/ENST00000624631/ENST00000624631.gff
create mode 100644 test/csq/ENST00000624631/ambiguous.txt
create mode 100644 test/csq/ENST00000624631/ambiguous.vcf
create mode 100644 test/csq/ENST00000624631/ascii-art.txt
create mode 100644 test/csq/ENST00000624631/segfault.txt.new
create mode 100755 test/csq/make-csq-test
create mode 100755 test/csq/sort-csq
create mode 100644 test/fill-tags-hemi.1.out
create mode 100644 test/fill-tags-hemi.2.out
copy test/{stats.b.vcf => fill-tags-hemi.vcf} (52%)
copy test/{view.vcf => fill-tags.3.out} (70%)
create mode 100644 test/fill-tags.3.smpl
create mode 100644 test/filter-missing-floats.vcf
create mode 100644 test/fixref.1.out
create mode 100644 test/fixref.vcf
create mode 100644 test/guess-ploidy.GL.out
create mode 100644 test/guess-ploidy.PL.out
create mode 100644 test/gvcf.merge.1.out
create mode 100644 test/gvcf.merge.1.vcf
create mode 100644 test/gvcf.merge.2.vcf
create mode 100644 test/gvcf.merge.3.vcf
delete mode 100644 test/large_chrom_tbi_limit.20.1.536870912.out
delete mode 100644 test/large_chrom_tbi_limit.vcf
create mode 100644 test/mendelian.1.out
create mode 100644 test/mendelian.2.out
copy test/{stats.b.vcf => mendelian.3.out} (54%)
create mode 100644 test/mendelian.vcf
create mode 100644 test/merge.5.a.vcf
create mode 100644 test/merge.5.b.vcf
create mode 100644 test/merge.5.out
copy test/{merge.abc.out => merge.abc.2.out} (93%)
copy test/{merge.abc.out => merge.abc.3.out} (71%)
create mode 100644 test/merge.gvcf.2.a.vcf
create mode 100644 test/merge.gvcf.2.b.vcf
create mode 100644 test/merge.gvcf.2.c.vcf
create mode 100644 test/merge.gvcf.2.out
create mode 100644 test/mpileup.2.samples
copy test/{mpileup.X.out => mpileup.X.2.out} (69%)
copy test/{mpileup.c.X.out => mpileup.c.X.2.out} (94%)
create mode 100644 test/mpileup/mpileup.1.bam
create mode 100644 test/mpileup/mpileup.1.bam.bai
create mode 100644 test/mpileup/mpileup.1.cram
create mode 100644 test/mpileup/mpileup.1.cram.crai
create mode 100644 test/mpileup/mpileup.1.out
create mode 100644 test/mpileup/mpileup.1.sam
create mode 100644 test/mpileup/mpileup.10.out
create mode 100644 test/mpileup/mpileup.11.out
create mode 100644 test/mpileup/mpileup.2.bam
create mode 100644 test/mpileup/mpileup.2.bam.bai
create mode 100644 test/mpileup/mpileup.2.cram
create mode 100644 test/mpileup/mpileup.2.cram.crai
create mode 100644 test/mpileup/mpileup.2.out
create mode 100644 test/mpileup/mpileup.2.sam
create mode 100644 test/mpileup/mpileup.3.bam
create mode 100644 test/mpileup/mpileup.3.bam.bai
create mode 100644 test/mpileup/mpileup.3.cram
create mode 100644 test/mpileup/mpileup.3.cram.crai
create mode 100644 test/mpileup/mpileup.3.out
create mode 100644 test/mpileup/mpileup.3.sam
create mode 100644 test/mpileup/mpileup.4.bam
create mode 100644 test/mpileup/mpileup.4.cram
create mode 100644 test/mpileup/mpileup.4.out
create mode 100644 test/mpileup/mpileup.4.sam
create mode 100644 test/mpileup/mpileup.5.out
create mode 100644 test/mpileup/mpileup.6.out
create mode 100644 test/mpileup/mpileup.7.out
create mode 100644 test/mpileup/mpileup.8.out
create mode 100644 test/mpileup/mpileup.9.out
create mode 100644 test/mpileup/mpileup.ref.fa
create mode 100644 test/mpileup/mpileup.ref.fa.fai
create mode 100644 test/mplp.10.samples
create mode 100644 test/mplp.11.rgs
create mode 100644 test/mplp.9.samples
create mode 100644 test/mplp.samples
copy test/{query.23.out => query.24.out} (65%)
create mode 100644 test/query.25.out
create mode 100644 test/query.26.out
create mode 100644 test/query.27.out
create mode 100644 test/query.28.out
create mode 100644 test/query.29.out
create mode 100644 test/query.30.out
create mode 100644 test/query.31.out
create mode 100644 test/query.32.out
create mode 100644 test/query.33.out
copy test/{query.filter.vcf => query.filter-type.vcf} (85%)
create mode 100644 test/query.filter.2.vcf
create mode 100644 test/ref.out
create mode 100644 test/ref.vcf
copy test/{plugin1.vcf => setGT.1.out} (80%)
copy test/{plugin1.vcf => setGT.vcf} (85%)
copy test/{stats.chk => stats.B.chk} (63%)
create mode 100644 test/test-regidx.c
create mode 100644 test/trio.out
create mode 100644 test/trio.ped
create mode 100644 test/trio.vcf
create mode 100644 test/view.GP.vcf
create mode 100644 test/view.GT.vcf
copy test/{view.10.out => view.GTsubset.NA1.out} (81%)
copy test/{view.6.out => view.GTsubset.NA1NA2.out} (83%)
copy test/{view.10.out => view.GTsubset.NA1NA2NA3.out} (86%)
create mode 100644 test/view.vectors.2.vcf
create mode 100644 test/view.vectors.C.out
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bcftools.git
More information about the debian-med-commit
mailing list