[med-svn] [bcftools] 01/02: Apply patch from upstream to reduce failing tests on different architectures. Addresses bug #870060
Andreas Tille
tille at debian.org
Wed Dec 13 15:01:37 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 1f25fabf64ec4a4191b6510936dd3a624a8dcda6
Author: Andreas Tille <tille at debian.org>
Date: Wed Dec 13 15:56:10 2017 +0100
Apply patch from upstream to reduce failing tests on different architectures. Addresses bug #870060
---
debian/changelog | 8 +
...e_test_cases_conform_to_VCF_specification.patch | 656 +++++++++++++++++++++
debian/patches/series | 1 +
3 files changed, 665 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index 857d2c9..1e92c6f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+bcftools (1.6-2) UNRELEASED; urgency=medium
+
+ * Team upload
+ * Apply patch from upstream to reduce failing tests on different
+ architectures. Addresses bug #870060
+
+ -- Andreas Tille <tille at debian.org> Wed, 13 Dec 2017 15:54:52 +0100
+
bcftools (1.6-1) experimental; urgency=medium
* Team upload.
diff --git a/debian/patches/make_the_test_cases_conform_to_VCF_specification.patch b/debian/patches/make_the_test_cases_conform_to_VCF_specification.patch
new file mode 100644
index 0000000..5c74576
--- /dev/null
+++ b/debian/patches/make_the_test_cases_conform_to_VCF_specification.patch
@@ -0,0 +1,656 @@
+From: Petr Danecek <pd3 at sanger.ac.uk>
+Date: Wed, 13 Dec 2017 12:58:37 +0000
+Subject: Make the test cases conform to VCF specification
+Origin: https://github.com/samtools/bcftools/commit/9a38c20d536b8893df6ac7e6cca845f205dda85e.patch
+Bug-Debian: https://bugs.debian.org/870060
+Bug-Upstream: https://github.com/samtools/bcftools/issues/720
+
+Most of these are cosmetic, but some are likely to fix at least some of the
+platform-dependant test failures reported in #720. Specifically the merging
+code relies on the correct number of fields in the FORMAT/Number=G tags.
+---
+ test/aa.out | 1 +
+ test/aa.vcf | 1 +
+ test/ad-bias.vcf | 1 +
+ test/annotate.out | 2 +-
+ test/annotate.vcf | 2 +-
+ test/annotate2.out | 2 +-
+ test/annotate3.out | 2 +-
+ test/annots.vcf | 2 +-
+ test/check.vcf | 5 +++--
+ test/consensus.vcf | 3 +++
+ test/consensus2.vcf | 5 +++++
+ test/convert.gt.vcf | 1 +
+ test/convert.gvcf.out | 1 +
+ test/convert.gvcf.vcf | 1 +
+ test/convert.vcf | 1 +
+ test/csq.vcf | 3 ++-
+ test/empty.vcf | 1 +
+ test/ex2.vcf | 4 ++--
+ test/fill-tags.2.out | 2 +-
+ test/fill-tags.3.out | 2 +-
+ test/filter-missing-floats.vcf | 1 +
+ test/filter.10.out | 1 +
+ test/filter.4.vcf | 1 +
+ test/fixref.2.out | 1 +
+ test/fixref.2a.vcf | 1 +
+ test/fixref.2b.vcf | 1 +
+ test/fixref.vcf | 1 +
+ test/gvcf.merge.1.out | 5 ++---
+ test/gvcf.merge.1.vcf | 4 ++--
+ test/gvcf.merge.2.vcf | 4 ++--
+ test/gvcf.merge.3.vcf | 4 ++--
+ test/idx.vcf | 1 +
+ test/isec.a.vcf | 6 +++++-
+ test/isec.tab.out | 10 +++++-----
+ test/many.alleles.trim.out | 1 +
+ test/many.alleles.vcf | 1 +
+ test/merge.2.a.vcf | 2 +-
+ test/merge.2.b.vcf | 4 ++--
+ test/merge.4.a.vcf | 4 ++--
+ test/merge.4.out | 4 ++--
+ test/merge.gvcf.2.a.vcf | 2 +-
+ test/merge.gvcf.2.out | 2 +-
+ test/plugin-missing2ref.out.vcf | 2 +-
+ test/regions.vcf | 14 +++++++-------
+ test/view.10.out | 2 +-
+ test/view.6.out | 2 +-
+ test/view.GL.vcf | 2 +-
+ test/view.GTsubset.NA1NA2NA3.out | 2 +-
+ test/view.PL.vcf | 2 +-
+ test/view.exclude.out | 2 +-
+ test/view.vcf | 2 +-
+ 51 files changed, 82 insertions(+), 51 deletions(-)
+
+--- a/test/aa.out
++++ b/test/aa.out
+@@ -1,5 +1,6 @@
+ ##fileformat=VCFv4.2
+ ##FILTER=<ID=PASS,Description="All filters passed">
++##reference=file://some/path/human_g1k_v37.fasta
+ ##contig=<ID=1,length=2147483647>
+ ##contig=<ID=2,length=2147483647>
+ ##contig=<ID=3,length=2147483647>
+--- a/test/aa.vcf
++++ b/test/aa.vcf
+@@ -1,5 +1,6 @@
+ ##fileformat=VCFv4.2
+ ##FILTER=<ID=PASS,Description="All filters passed">
++##reference=file://some/path/human_g1k_v37.fasta
+ ##contig=<ID=1,length=2147483647>
+ ##contig=<ID=2,length=2147483647>
+ ##contig=<ID=3,length=2147483647>
+--- a/test/ad-bias.vcf
++++ b/test/ad-bias.vcf
+@@ -1,5 +1,6 @@
+ ##fileformat=VCFv4.2
+ ##FILTER=<ID=PASS,Description="All filters passed">
++##reference=file://some/path/human_g1k_v37.fasta
+ ##contig=<ID=22,length=51304566>
+ ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths">
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+--- a/test/annotate.out
++++ b/test/annotate.out
+@@ -39,5 +39,5 @@
+ 2 3199812 indel_3199812 G GTT,GT 82.7 PASS AN=4;AC=2,2;INDEL GT:GQ:DP 1/2:322:26 1/2:322:26
+ 3 3212016 indel_3212016 CTT C,CT 79 PASS AN=4;AC=2,2;INDEL GT:GQ:DP 1/2:91:26 1/2:91:26
+ 4 3258448 indel_3258448 TACACACAC T 59.9 PASS AN=4;AC=2;INDEL GT:GQ:DP 0/1:325:31 0/1:325:31
+-4 4000000 id1 T A,C 59.9 PASS AN=4;AC=2;INDEL GT:GQ:DP 0/1:325:31 0/1:325:31
++4 4000000 id1 T A,C 59.9 PASS AN=4;AC=2,0;INDEL GT:GQ:DP 0/1:325:31 0/1:325:31
+ 4 4000001 id2 T A 59.9 PASS AN=4;AC=2;INDEL GT:GQ:DP 0/1:325:31 0/1:325:31
+--- a/test/annotate.vcf
++++ b/test/annotate.vcf
+@@ -35,5 +35,5 @@
+ 2 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26
+ 3 3212016 . CTT C,CT 79 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26
+ 4 3258448 . TACACACAC T 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
+-4 4000000 . T A,C 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
++4 4000000 . T A,C 59.9 PASS AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31
+ 4 4000001 . T A 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
+--- a/test/annotate2.out
++++ b/test/annotate2.out
+@@ -39,5 +39,5 @@
+ 2 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26
+ 3 3212016 . CTT C,CT 79 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26
+ 4 3258448 . TACACACAC T 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
+-4 4000000 . T A,C 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
++4 4000000 . T A,C 59.9 PASS AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31
+ 4 4000001 . T A 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
+--- a/test/annotate3.out
++++ b/test/annotate3.out
+@@ -36,5 +36,5 @@
+ 2 3199812 id11 G GTT,GT 99 PASS AN=4;AC=2,2;STR=id11 GT:GQ:DP 1/2:322:26 1/2:322:26
+ 3 3212016 id12 CTT C,CT 99 PASS AN=4;AC=2,2;STR=id12 GT:GQ:DP 1/2:91:26 1/2:91:26
+ 4 3258448 id13 TACACACAC T 99 PASS AN=4;AC=2;STR=id13 GT:GQ:DP 0/1:325:31 0/1:325:31
+-4 4000000 . T A,C 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
++4 4000000 . T A,C 59.9 PASS AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31
+ 4 4000001 . T A 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
+--- a/test/annots.vcf
++++ b/test/annots.vcf
+@@ -27,7 +27,7 @@
+ 1 3062915 idSNP G T,C 99 PASS STR=testSNP;TEST=5;DP4=1,2,3,4;AN=3;AC=0,0 GT:TT:GQ:DP:GL 0|0:9,9:999:99:-99,-9,-99,-99,-9,-99 0:9,9:999:99:-99,-9,-99
+ 1 3106154 id4 CAAA C 99 PASS STR=id4;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99
+ 1 3106154 id5 C CT 99 PASS STR=id5;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99
+-1 3157410 id6 GA GC,G 99 PASS STR=id6;AN=4;AC=0 GT:GQ:DP 0|0:99:99 0|0:99:99
++1 3157410 id6 GA GC,G 99 PASS STR=id6;AN=4;AC=0,0 GT:GQ:DP 0|0:99:99 0|0:99:99
+ 1 3162006 id7 GAA GG 99 PASS STR=id7;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99
+ 1 3177144 id8 G T 99 PASS STR=id8;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99
+ 1 3177144 id9 G . 99 PASS STR=id9;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99
+--- a/test/check.vcf
++++ b/test/check.vcf
+@@ -12,6 +12,7 @@
+ ##contig=<ID=1,assembly=b37,length=249250621>
+ ##contig=<ID=3,assembly=b37,length=198022430>
+ ##contig=<ID=4,assembly=b37,length=191154276>
++##contig=<ID=2,assembly=b37,length=191154276>
+ ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+ ##readme=AAAAAA
+ ##readme=BBBBBB
+@@ -29,8 +30,8 @@
+ 2 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26
+ 3 3212016 . CTT C,CT 79 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26
+ 4 3258448 . TACACACAC T 59.9 PASS DP=62;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
+-4 3258449 . GCAAA GA,G 59.9 PASS DP=62;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
+-4 3258450 . AAAAGAAAAAG A,AAAAAAG 59.9 PASS DP=60;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
++4 3258449 . GCAAA GA,G 59.9 PASS DP=62;AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31
++4 3258450 . AAAAGAAAAAG A,AAAAAAG 59.9 PASS DP=60;AN=4;AC=2,0 GT:GQ:DP 0/1:325:31 0/1:325:31
+ 4 3258451 . AAA AGT 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
+ 4 3258452 . AAA AGA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
+ 4 3258453 . AACA AGA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
+--- a/test/consensus.vcf
++++ b/test/consensus.vcf
+@@ -1,7 +1,10 @@
+ ##fileformat=VCFv4.2
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
++##reference=file://some/path/human_g1k_v37.fasta
+ ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+ ##ALT=<ID=DEL,Description="Deletion">
++##contig=<ID=1,assembly=b37,length=249250621>
++##contig=<ID=2,assembly=b37,length=249250621>
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA001
+ 1 5 . C a . PASS . GT 0/1
+ 1 5 . C t . PASS . GT 0/1
+--- a/test/consensus2.vcf
++++ b/test/consensus2.vcf
+@@ -2,6 +2,11 @@
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+ ##ALT=<ID=DEL,Description="Deletion">
++##reference=file://some/path/human_g1k_v37.fasta
++##contig=<ID=1,assembly=b37,length=249250621>
++##contig=<ID=2,assembly=b37,length=249250621>
++##contig=<ID=3,assembly=b37,length=249250621>
++##contig=<ID=4,assembly=b37,length=249250621>
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA001
+ 1 59 . C a,Caa . PASS . GT 1|2
+ 2 60 . C a,Caa . PASS . GT 1|2
+--- a/test/convert.gt.vcf
++++ b/test/convert.gt.vcf
+@@ -1,6 +1,7 @@
+ ##fileformat=VCFv4.1
+ ##FILTER=<ID=PASS,Description="All filters passed">
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
++##reference=file://some/path/human_g1k_v37.fasta
+ ##contig=<ID=X,assembly=b37,length=155270560>
+ ##bcftools_normVersion=1.2+htslib-1.2.1
+ ##bcftools_normCommand=norm -m - convert.vcf
+--- a/test/convert.gvcf.out
++++ b/test/convert.gvcf.out
+@@ -1,5 +1,6 @@
+ ##fileformat=VCFv4.1
+ ##FILTER=<ID=PASS,Description="All filters passed">
++##reference=file://some/path/human_g1k_v37.fasta
+ ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+--- a/test/convert.gvcf.vcf
++++ b/test/convert.gvcf.vcf
+@@ -1,5 +1,6 @@
+ ##fileformat=VCFv4.1
+ ##FILTER=<ID=PASS,Description="All filters passed">
++##reference=file://some/path/human_g1k_v37.fasta
+ ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+--- a/test/convert.vcf
++++ b/test/convert.vcf
+@@ -1,5 +1,6 @@
+ ##fileformat=VCFv4.1
+ ##FILTER=<ID=PASS,Description="All filters passed">
++##reference=file://some/path/human_g1k_v37.fasta
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+ ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Estimated Genotype Probability">
+--- a/test/csq.vcf
++++ b/test/csq.vcf
+@@ -1,6 +1,7 @@
+ ##fileformat=VCFv4.2
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+-##INFO=<ID=EXP,Number=1,Type=String,Description="Expected consequence">
++##reference=file://some/path/human_g1k_v37.fasta
++##INFO=<ID=EXP,Number=.,Type=String,Description="Expected consequence">
+ ##contig=<ID=1,length=2147483647>
+ ##contig=<ID=2,length=2147483647>
+ ##contig=<ID=3,length=2147483647>
+--- a/test/empty.vcf
++++ b/test/empty.vcf
+@@ -3,4 +3,5 @@
+ ##contig=<ID=20,length=63025520>
+ ##contig=<ID=X,length=155270560>
+ ##contig=<ID=Y,length=59373566>
++##reference=file://some/path/human_g1k_v37.fasta
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+--- a/test/ex2.vcf
++++ b/test/ex2.vcf
+@@ -7,14 +7,14 @@
+ ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+ ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+ ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+-##INFO=<ID=HOMSEQ,Number=.,Type=String>
++##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="testing">
+ ##FILTER=<ID=q10,Description="Quality below 10">
+ ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+ ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+-##FORMAT=<ID=CNL,Number=.,Type=Integer>
++##FORMAT=<ID=CNL,Number=.,Type=Integer,Description="Some description">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+ 20 14370 rs6054257 G A 29.1 . NS=3;DP=14;AF=0.5;HOMSEQ;DB GT:GQ:DP:HQ:CNL 0|0:48:1:25,30:10,20 1|0:48:8:49,51:. ./.:43:5:.,.:1
+ 20 17330 . T A . q10;s50 NS=3;DP=11;AF=0.017;H2 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:4,5
+--- a/test/fill-tags.2.out
++++ b/test/fill-tags.2.out
+@@ -33,7 +33,7 @@
+ ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency">
+ ##INFO=<ID=MAF,Number=A,Type=Float,Description="Minor Allele frequency">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+-11 2343543 . A . 999 PASS DP=100223;NS=3;AN=6 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99
++11 2343543 . A . 999 PASS DP=100223;NS=3;AN=6 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99
+ 11 5464562 . C T 999 PASS DP=0;NS=0;AN=0;AC=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:.
+ 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31;NS=3;AN=6;AF=0.833333;MAF=0.166667;AC=5 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 1/1:255,255,0:182:99
+ 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4;NS=3;AF=0.666667;MAF=0.333333 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 1/1:78:99:255,213,0
+--- a/test/fill-tags.3.out
++++ b/test/fill-tags.3.out
+@@ -32,7 +32,7 @@
+ ##INFO=<ID=AC_AB,Number=A,Type=Integer,Description="Allele count in genotypes in AB">
+ ##INFO=<ID=AC_BC,Number=A,Type=Integer,Description="Allele count in genotypes in BC">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+-11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99
++11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99
+ 11 5464562 . C T 999 PASS DP=0;AC_AB=0;AC_BC=0;AC=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:.
+ 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31;AC_AB=3;AC_BC=4;AC=5 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 1/1:255,255,0:182:99
+ 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4;AC_AB=2;AC_BC=3 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 1/1:78:99:255,213,0
+--- a/test/filter-missing-floats.vcf
++++ b/test/filter-missing-floats.vcf
+@@ -1,4 +1,5 @@
+ ##fileformat=VCFv4.2
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##contig=<ID=1,length=249250621>
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##INFO=<ID=A_AF,Number=A,Type=Float,Description="Allele frequency">
+--- a/test/filter.10.out
++++ b/test/filter.10.out
+@@ -1,5 +1,6 @@
+ ##fileformat=VCFv4.1
+ ##FILTER=<ID=PASS,Description="All filters passed">
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##contig=<ID=chr1,length=135006516>
+ ##INFO=<ID=TEST1,Number=1,Type=Integer,Description="Test1">
+ ##INFO=<ID=TEST2,Number=1,Type=Float,Description="Test2">
+--- a/test/filter.4.vcf
++++ b/test/filter.4.vcf
+@@ -1,4 +1,5 @@
+ ##fileformat=VCFv4.1
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##contig=<ID=chr1,length=135006516>
+ ##INFO=<ID=TEST1,Number=1,Type=Integer,Description="Test1">
+ ##INFO=<ID=TEST2,Number=1,Type=Float,Description="Test2">
+--- a/test/fixref.2.out
++++ b/test/fixref.2.out
+@@ -1,5 +1,6 @@
+ ##fileformat=VCFv4.2
+ ##FILTER=<ID=PASS,Description="All filters passed">
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##contig=<ID=1,length=2147483647>
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001
+--- a/test/fixref.2a.vcf
++++ b/test/fixref.2a.vcf
+@@ -1,4 +1,5 @@
+ ##fileformat=VCFv4.2
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##contig=<ID=1,length=2147483647>
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001
+--- a/test/fixref.2b.vcf
++++ b/test/fixref.2b.vcf
+@@ -1,4 +1,5 @@
+ ##fileformat=VCFv4.2
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##contig=<ID=1,length=2147483647>
+ #CHROM POS ID REF ALT QUAL FILTER INFO
+--- a/test/fixref.vcf
++++ b/test/fixref.vcf
+@@ -1,4 +1,5 @@
+ ##fileformat=VCFv4.2
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##FILTER=<ID=PASS,Description="All filters passed">
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##contig=<ID=1,length=2147483647>
+--- a/test/gvcf.merge.1.out
++++ b/test/gvcf.merge.1.out
+@@ -1,10 +1,10 @@
+ ##fileformat=VCFv4.1
+ ##FILTER=<ID=PASS,Description="All filters passed">
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30 or not present">
+ ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.3">
+ ##FILTER=<ID=nc,Description="No-call">
+-##contig=<ID=chrY,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
+-##contig=<ID=chrM,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens">
++##contig=<ID=chr1,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+ ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
+@@ -22,7 +22,6 @@
+ ##INFO=<ID=CGA_FI,Number=A,Type=String,Description="Functional impact annotation">
+ ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the region described in this record">
+ ##INFO=<ID=BLOCKAVG_min30p3a,Number=0,Type=Flag,Description="Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y], y <= max(x+3,(x*1.3)). All printed site block sample values are the minimum observed in the region spanned by the block">
+-##contig=<ID=chr1>
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G06 D05 H09
+ chr1 10106 . C . 0 LowGQX BLOCKAVG_min30p3a;AN=2 GT:GQX:DP:DPF ./.:.:.:. 0/0:12:5:0 ./.:.:.:.
+ chr1 10107 . C . 0 LowGQX;HighDPFRatio BLOCKAVG_min30p3a;AN=4 GT:GQX:DP:DPF .:.:0:1 0/0:12:5:0 0/0:5:2:0
+--- a/test/gvcf.merge.1.vcf
++++ b/test/gvcf.merge.1.vcf
+@@ -1,10 +1,10 @@
+ ##fileformat=VCFv4.1
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##FILTER=<ID=PASS,Description="All filters passed">
+ ##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30 or not present">
+ ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.3">
+ ##FILTER=<ID=nc,Description="No-call">
+-##contig=<ID=chrY,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
+-##contig=<ID=chrM,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens">
++##contig=<ID=chr1,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+ ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
+--- a/test/gvcf.merge.2.vcf
++++ b/test/gvcf.merge.2.vcf
+@@ -1,10 +1,10 @@
+ ##fileformat=VCFv4.1
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##FILTER=<ID=PASS,Description="All filters passed">
+ ##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30 or not present">
+ ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.3">
+ ##FILTER=<ID=nc,Description="No-call">
+-##contig=<ID=chrY,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
+-##contig=<ID=chrM,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens">
++##contig=<ID=chr1,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+ ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
+--- a/test/gvcf.merge.3.vcf
++++ b/test/gvcf.merge.3.vcf
+@@ -1,10 +1,10 @@
+ ##fileformat=VCFv4.1
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##FILTER=<ID=PASS,Description="All filters passed">
+ ##FILTER=<ID=LowGQX,Description="Locus GQX is less than 30 or not present">
+ ##FILTER=<ID=HighDPFRatio,Description="The fraction of basecalls filtered out at a site is greater than 0.3">
+ ##FILTER=<ID=nc,Description="No-call">
+-##contig=<ID=chrY,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
+-##contig=<ID=chrM,length=16569,assembly=B37,md5=c68f52674c9fb33aef52dcf399755519,species="Homo sapiens">
++##contig=<ID=chr1,length=59373566,assembly=B37,md5=1e86411d73e6f00a10590f976be01623,species="Homo sapiens">
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+ ##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
+--- a/test/idx.vcf
++++ b/test/idx.vcf
+@@ -1,4 +1,5 @@
+ ##fileformat=VCFv4.1
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##contig=<ID=1,length=249250621>
+ ##contig=<ID=11,length=135006516>
+ ##contig=<ID=20,length=63025520>
+--- a/test/isec.a.vcf
++++ b/test/isec.a.vcf
+@@ -6,6 +6,10 @@
+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+ ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+ ##FILTER=<ID=q10,Description="Quality below 10">
++##contig=<ID=1,length=249250621>
++##contig=<ID=2,length=249250621>
++##contig=<ID=3,length=249250621>
++##contig=<ID=4,length=249250621>
+ ##test=<xx=A,yy=B,zz=C>
+ ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+ ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+@@ -16,7 +20,7 @@
+ 1 3062915 . GTTT G 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
+ 1 3062915 . G T 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
+ 1 3106154 . CAAA C 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32
+-1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32
++1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1,0 GT:GQ:DP 0/1:245:32
+ 1 3157410 . GA G 628 q10 DP=21;AN=2;AC=2 GT:GQ:DP 1/1:21:21
+ 1 3162006 . GAA G 1016 PASS DP=22;AN=2;AC=1 GT:GQ:DP 0/1:212:22
+ 1 3177144 . GT G 727 PASS DP=30;AN=2;AC=1 GT:GQ:DP 0/1:150:30
+--- a/test/isec.tab.out
++++ b/test/isec.tab.out
+@@ -7,21 +7,21 @@
+ ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+ ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+ ##FILTER=<ID=q10,Description="Quality below 10">
++##contig=<ID=1,length=249250621>
++##contig=<ID=2,length=249250621>
++##contig=<ID=3,length=249250621>
++##contig=<ID=4,length=249250621>
+ ##test=<xx=A,yy=B,zz=C>
+ ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+ ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+ ##readme=AAAAAA
+ ##readme=BBBBBB
+-##contig=<ID=1>
+-##contig=<ID=2>
+-##contig=<ID=3>
+-##contig=<ID=4>
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A
+ 1 3062915 . GTTT G 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
+ 1 3062915 . G T 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
+ 1 3106154 . CAAA C 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32
+-1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32
++1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1,0 GT:GQ:DP 0/1:245:32
+ 1 3157410 . GA G 628 q10 DP=21;AN=2;AC=2 GT:GQ:DP 1/1:21:21
+ 1 3162006 . GAA G 1016 PASS DP=22;AN=2;AC=1 GT:GQ:DP 0/1:212:22
+ 1 3177144 . GT G 727 PASS DP=30;AN=2;AC=1 GT:GQ:DP 0/1:150:30
+--- a/test/many.alleles.trim.out
++++ b/test/many.alleles.trim.out
+@@ -1,5 +1,6 @@
+ ##fileformat=VCFv4.1
+ ##FILTER=<ID=PASS,Description="All filters passed">
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##contig=<ID=chr7>
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+--- a/test/many.alleles.vcf
++++ b/test/many.alleles.vcf
+@@ -1,4 +1,5 @@
+ ##fileformat=VCFv4.1
++##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
+ ##contig=<ID=chr7>
+ ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR1528791
+--- a/test/merge.2.a.vcf
++++ b/test/merge.2.a.vcf
+@@ -27,4 +27,4 @@
+ 1 3106154 . C A 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
+ 1 3200000 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
+ 1 3200010 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
+-1 3200020 . C G,T 59.2 PASS AN=4;AC=2 GT:GL ./.:1,2,3,4,5,6 .:1,2,3
++1 3200020 . C G,T 59.2 PASS AN=0;AC=0,0 GT:GL ./.:1,2,3,4,5,6 .:1,2,3
+--- a/test/merge.2.b.vcf
++++ b/test/merge.2.b.vcf
+@@ -26,5 +26,5 @@
+ 1 3106154 . C CCC 342 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
+ 1 3106154 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
+ 1 3200000 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
+-1 3200010 . c A,T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
+-1 3200020 . C T,G 59.2 PASS AN=4;AC=2 GT:GL ./.:1,4,6,2,5,3 .:1,3,2
++1 3200010 . c A,T 59.2 PASS AN=4;AC=2,0 GT:GQ:DP 0/1:245:32 0/1:245:32
++1 3200020 . C T,G 59.2 PASS AN=0;AC=0,0 GT:GL ./.:1,4,6,2,5,3 .:1,3,2
+--- a/test/merge.4.a.vcf
++++ b/test/merge.4.a.vcf
+@@ -29,5 +29,5 @@
+ 1 3000000 id1 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GQ:XR:XA:XG 0/1:245:0,1:1:0,1,2 0/1:245:1,2:2:0,1,2
+ 1 3000000 . C CCG 59.2 PASS AN=4;AC=2 GT:GQ:XR:XA:XG 0/1:245:1,2:2:0,1,2 0/1:245:2,3:3:1,2,3
+ 1 3000002 . C CCG 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245
+-1 3000002 id2 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245:.:.:. 0/1:245:.:.:.
+-1 3000002 id3 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245:.:.:. 0/1:245:.
++1 3000002 id2 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245,0,199:.:.:. 0/1:245,0,199:.:.:.
++1 3000002 id3 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245,0,245:.:.:. 0/1:245,0,245:.
+--- a/test/merge.4.out
++++ b/test/merge.4.out
+@@ -30,5 +30,5 @@
+ 1 3000000 id1 C CCG,A 59.2 PASS TR=1,2,2;TA=1,1;TG=1,2,3,2,.,3;AN=8;AC=2,2 GT:GQ:XR:XA:XG 0/1:245:0,1,.:1,.:0,1,2,.,.,. 0/1:245:1,2,.:2,.:0,1,2,.,.,. 0/2:245:4,.,5:.,5:3,.,.,4,.,5 0/2:245:6,.,7:.,7:6,.,.,7,.,8
+ 1 3000000 . C CCG,A 59.2 PASS AN=8;AC=2,2 GT:GQ:XR:XA:XG 0/1:245:1,2,.:2,.:0,1,2,.,.,. 0/1:245:2,3,.:3,.:1,2,3,.,.,. 0/2:245:.:.:. 0/2:245:.:.:.
+ 1 3000002 . C CCG,A 59.2 PASS AN=8;AC=2,2 GT:GQ 0/1:245 0/1:245 0/2:245 0/2:245
+-1 3000002 id2 C CCG,A 59.2 PASS TR=1,2,2;TA=1,1;TG=1,2,3,2,.,3;AN=8;AC=2,2 GT:GL:XR:XA:XG:GQ 0/1:245,245,-1.56481e-39,.,.,.:.:.:.:. 0/1:245,-1.56481e-39,1.09706e-28,.,.,.:.:.:.:. 0/2:.:.:.:.:245 0/2:.:.:.:.:245
+-1 3000002 id3 C CCG,A 59.2 PASS TR=1,2,2;TA=1,1;TG=1,2,3,2,.,3;AN=8;AC=2,2 GT:GL:XR:XA:XG:GQ 0/1:245,245,-1.56481e-39,.,.,.:.:.:.:. 0/1:245,-1.56481e-39,1.09706e-28,.,.,.:.:.:.:. 0/2:.:.:.:.:245 0/2:.:1,.,2:.,2:1,.,.,2,.,3:245
++1 3000002 id2 C CCG,A 59.2 PASS TR=1,2,2;TA=1,1;TG=1,2,3,2,.,3;AN=8;AC=2,2 GT:GL:XR:XA:XG:GQ 0/1:245,0,199,.,.,.:.:.:.:. 0/1:245,0,199,.,.,.:.:.:.:. 0/2:.:.:.:.:245 0/2:.:.:.:.:245
++1 3000002 id3 C CCG,A 59.2 PASS TR=1,2,2;TA=1,1;TG=1,2,3,2,.,3;AN=8;AC=2,2 GT:GL:XR:XA:XG:GQ 0/1:245,0,245,.,.,.:.:.:.:. 0/1:245,0,245,.,.,.:.:.:.:. 0/2:.:.:.:.:245 0/2:.:1,.,2:.,2:1,.,.,2,.,3:245
+--- a/test/merge.gvcf.2.a.vcf
++++ b/test/merge.gvcf.2.a.vcf
+@@ -24,7 +24,7 @@
+ 3 1 . C <*> 0 . END=10;MinDP=33;QS=0.75,0.25 PL:DP:DV 0,4,10:4:1
+ 1 1619670 . C <*> 0 . END=1619877;MinDP=33;QS=0.75,0.25 PL:DP:DV 0,4,10:4:1
+ 4 20000975 . C <*> 0 . END=20001070;MinDP=33;QS=0.75,0.25 PL:DP:DV 0,4,10:4:1
+-4 20001071 . T G,<*> 0 . . PL:DP:DV 0,4,10:4:1
++4 20001071 . T G,<*> 0 . . PL:DP:DV 0,4,10,20,30,40:4:1
+ 5 110285 . TAACCCC T . . . PL 89,6,0
+ 5 1110285 . T TAACCCC . . . PL 89,6,0
+ 6 600 . T A . . END=666 PL 66,1,1
+--- a/test/merge.gvcf.2.out
++++ b/test/merge.gvcf.2.out
+@@ -31,7 +31,7 @@
+ 1 1619789 . N <*> 0 . END=1619877;MinDP=33;QS=0.75,0.25 PL:DP:DV 0,4,10:4:1 .:.:. .:.:.
+ 4 20000975 . C <*> 0 . END=20001021;MinDP=33;QS=0.75,0.25 PL:DP:DV 0,4,10:4:1 .:.:. .:.:.
+ 4 20001022 . C <*> 0 . END=20001070;MinDP=33;QS=1.5,0.5 PL:DP:DV 0,4,10:4:1 0,4,10:4:1 .:.:.
+-4 20001071 . T G,<*> 0 . QS=0.75,0.25,0 PL:DP:DV 0,4,10:4:1 0,4,10,35,73,113:4:1 .:.:.
++4 20001071 . T G,<*> 0 . QS=0.75,0.25,0 PL:DP:DV 0,4,10,20,30,40:4:1 0,4,10,35,73,113:4:1 .:.:.
+ 5 110285 . T C,<*> . . . PL . 114,0,15,35,73,113 .
+ 5 110285 . TAACCCC T . . . PL 89,6,0 . .
+ 5 1110285 . T C,<*> . . . PL . 114,0,15,35,73,113 .
+--- a/test/plugin-missing2ref.out.vcf
++++ b/test/plugin-missing2ref.out.vcf
+@@ -24,7 +24,7 @@
+ 1 3000150 . C T 59.2 PASS . GT:GQ 1|1:245 1|1:245 0/1:245 1/1:245
+ 1 3000151 . C T 59.2 PASS . GT:DP:GQ 0|0:32:245 0|0:32:245 0|0:32:245 0|0:32:245
+ 1 3062915 id3D GTTT G 12.9 q10 DP4=1,2,3,4;INDEL;STR=test GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20
+-1 3062915 idSNP G T,C 12.6 test TEST=5;DP4=1,2,3,4 GT:TT:GQ:DP:GL 0/1:0,1:409:35:-20,-5,-20,-20,-5,-20 2:0,1:409:35:-20,-5,-20 2/2:0,1:409:35:-20,-5,-20 2|2:0,1:409:35:-20,-5,-20
++1 3062915 idSNP G T,C 12.6 test TEST=5;DP4=1,2,3,4 GT:TT:GQ:DP:GL 0/1:0,1:409:35:-20,-5,-20,-20,-5,-20 2:0,1:409:35:-20,-5,-20 2/2:0,1:409:35:-20,-5,-20,-20,-5,-20 2|2:0,1:409:35:-20,-5,-20,-20,-5,-20
+ 2 3199812 . G GTT,GT 82.7 PASS . GT:GQ:DP 0|0:322:26 0|0:322:26 0|0:322:26 0|0:322:26
+ 3 3212016 . CTT C,CT 79 PASS . GT:GQ:DP 0|0:91:26 0|0:91:26 0|0:91:26 0|0:91:26
+ 4 3258448 . TACACACAC T 59.9 PASS . GT:GQ:DP 0|0:325:31 0|0:325:31 0|0:325:31 0|0:325:31
+--- a/test/regions.vcf
++++ b/test/regions.vcf
+@@ -17,13 +17,13 @@
+ 1 3062915 . GTT G 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
+ 1 3062915 . G T 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
+ 1 3106154 . CA C 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32
+-1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32
++1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1,0 GT:GQ:DP 0/1:245:32
+ 1 3157410 . G A 628 q10 DP=21;AN=2;AC=2 GT:GQ:DP 1/1:21:21
+ 1 3162006 . G A 1016 PASS DP=22;AN=2;AC=1 GT:GQ:DP 0/1:212:22
+ 1 3177144 . GT G 727 PASS DP=30;AN=2;AC=1 GT:GQ:DP 0/1:150:30
+-1 3184885 . T TA 246 PASS DP=10;AN=2;AC=1,1 GT:GQ:DP 1/2:12:10
+-2 3199812 . G T 481 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:322:26
+-2 3199815 . C T 481 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:322:26
+-3 3212016 . C A 565 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:91:26
+-3 3212026 . C A 565 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:91:26
+-3 3212036 . C A 565 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:91:26
++1 3184885 . T TA 246 PASS DP=10;AN=2;AC=1 GT:GQ:DP 1/2:12:10
++2 3199812 . G T 481 PASS DP=26;AN=2;AC=1 GT:GQ:DP 1/2:322:26
++2 3199815 . C T 481 PASS DP=26;AN=2;AC=1 GT:GQ:DP 1/2:322:26
++3 3212016 . C A 565 PASS DP=26;AN=2;AC=1 GT:GQ:DP 1/2:91:26
++3 3212026 . C A 565 PASS DP=26;AN=2;AC=1 GT:GQ:DP 1/2:91:26
++3 3212036 . C A 565 PASS DP=26;AN=2;AC=1 GT:GQ:DP 1/2:91:26
+--- a/test/view.10.out
++++ b/test/view.10.out
+@@ -30,7 +30,7 @@
+ ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+ ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+-11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99
++11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99
+ 11 5464562 . C T 999 PASS DP=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:.
+ X 3048719 . T C 999 PASS DP4=13263,27466,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=4;AC=3 GT:PL:DP:GQ 0:0,255:20:99 1:255,0:33:99 0|1:255,0,157:52:99
+ Y 8657215 . C A 999 PASS DP4=74915,114274,1948,2955;DP=195469;Dels=0;FS=3.181;MQ0=0;MQ=50;PV4=0.86,1,0,1;QD=33.77;AN=2;AC=1 GT:PL:DP:GQ 0:0,255:47:99 1:255,0:64:99 .:.:.:.
+--- a/test/view.6.out
++++ b/test/view.6.out
+@@ -30,7 +30,7 @@
+ ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+ ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+-11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99
++11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99
+ 11 5464562 . C T 999 PASS DP=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:.
+ 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 1/1:255,255,0:182:99
+ 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 1/1:78:99:255,213,0
+--- a/test/view.GL.vcf
++++ b/test/view.GL.vcf
+@@ -12,7 +12,7 @@
+ ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+ ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+-11 2343543 . A . 999 PASS . GL 0,-25.5,-25.5 0,-25.5,-25.5 0,-25.5,-25.5
++11 2343543 . A . 999 PASS . GL 0 0 0
+ 11 5464562 . C T 999 PASS . GL 0,0,0 0,0,0 0,0,0
+ 20 76962 rs6111385 T C 999 PASS . GL -25.5,0,-25.5 -25.5,-25.5,0 -25.5,-25.5,0
+ 20 126310 . ACC A 999 StrandBias;EndDistBias . GL -25.5,0,-13.2 -25.5,0,-13.9 -25.5,-21.3,0
+--- a/test/view.GTsubset.NA1NA2NA3.out
++++ b/test/view.GTsubset.NA1NA2NA3.out
+@@ -30,7 +30,7 @@
+ ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+ ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+-11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99
++11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99
+ 11 5464562 . C T 999 PASS DP=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:.
+ 20 326891 . A AC 999 PASS DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=4;AC=2 GT:DP:GQ:PL 0|1:117:99:255,0,132 0|1:111:99:255,0,139 ./.:.:.:.,.,.
+ Y 10011673 rs78249411 G A 999 MinAB DP4=47351,30839,178796,279653;DP=550762;Dels=0;FS=41.028;MQ0=37362;MQ=26;PV4=0,0,0,1;QD=17.45;AN=2;AC=2 GT:PL:DP:GQ 1:126,101:146:37 1:95,0:130:99 .:.:.:.
+--- a/test/view.PL.vcf
++++ b/test/view.PL.vcf
+@@ -12,7 +12,7 @@
+ ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+ ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred scaled genotype likelihoods">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+-11 2343543 . A . 999 PASS . PL 0,255,255 0,255,255 0,255,255
++11 2343543 . A . 999 PASS . PL 0 0 0
+ 11 5464562 . C T 999 PASS . PL 0,0,0 0,0,0 0,0,0
+ 20 76962 rs6111385 T C 999 PASS . PL 255,0,255 255,255,0 255,255,0
+ 20 126310 . ACC A 999 StrandBias;EndDistBias . PL 255,0,132 255,0,139 255,213,0
+--- a/test/view.exclude.out
++++ b/test/view.exclude.out
+@@ -30,7 +30,7 @@
+ ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+ ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002
+-11 2343543 . A . 999 PASS DP=100223;AN=4 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99
++11 2343543 . A . 999 PASS DP=100223;AN=4 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99
+ 11 5464562 . C T 999 PASS DP=0;AC=0;AN=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:.
+ 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31;AC=3;AN=4 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99
+ 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=4;AC=2 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139
+--- a/test/view.vcf
++++ b/test/view.vcf
+@@ -29,7 +29,7 @@
+ ##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+ ##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+-11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0,255,255:193:99 0/0:0,255,255:211:99 0/0:0,255,255:182:99
++11 2343543 . A . 999 PASS DP=100223 GT:PL:DP:GQ 0/0:0:193:99 0/0:0:211:99 0/0:0:182:99
+ 11 5464562 . C T 999 PASS DP=0 GT:PL:DP:GQ ./.:0,0,0:.:. ./.:0,0,0:.:. ./.:0,0,0:.:.
+ 20 76962 rs6111385 T C 999 PASS DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31 GT:PL:DP:GQ 0/1:255,0,255:193:99 1/1:255,255,0:211:99 1/1:255,255,0:182:99
+ 20 126310 . ACC A 999 StrandBias;EndDistBias DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4 GT:DP:GQ:PL 0/1:117:99:255,0,132 0/1:111:99:255,0,139 1/1:78:99:255,213,0
diff --git a/debian/patches/series b/debian/patches/series
index 450663e..d2ec1c2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
tests-pluginpath.patch
test-regidx-unsigned-char.patch
fix-test_vcf_query.patch
+make_the_test_cases_conform_to_VCF_specification.patch
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bcftools.git
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