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Fix up bad paths to public/testdata files

This commit is contained in:
Mark DePristo 2012-05-24 10:54:27 -04:00
parent e9c22b9aad
commit 57a1ac0888
19 changed files with 23 additions and 35 deletions
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public/testdata/inttestbgl.gprobs → public/testdata/Beagle/inttestbgl.gprobs vendored
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public/testdata/inttestbgl.input.vcf → public/testdata/Beagle/inttestbgl.input.vcf vendored
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public/testdata/inttestbgl.like → public/testdata/Beagle/inttestbgl.like vendored
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public/testdata/inttestbgl.output.vcf → public/testdata/Beagle/inttestbgl.output.vcf vendored
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public/testdata/inttestbgl.phased → public/testdata/Beagle/inttestbgl.phased vendored
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public/testdata/inttestbgl.r2 → public/testdata/Beagle/inttestbgl.r2 vendored
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public/testdata/PhaseByTransmission.IntegrationTest.FP.vcf → public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.FP.vcf vendored
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public/testdata/PhaseByTransmission.IntegrationTest.Special.vcf → public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.Special.vcf vendored
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public/testdata/PhaseByTransmission.IntegrationTest.TN.vcf → public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TN.vcf vendored
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public/testdata/PhaseByTransmission.IntegrationTest.TP.vcf → public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TP.vcf vendored
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public/testdata/PhaseByTransmission.IntegrationTest.goodFamilies.ped → public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.goodFamilies.ped vendored
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public/testdata/ROD_validation/always_reindex.vcf vendored
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@ -1,7 +0,0 @@
##fileformat=VCFv4.0
##fileDate=20090908
##source=QCALLv1.0
##reference=1000GenomesPilot-NCBI36
##phasing=partial
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA06985 NA06986 NA06994 NA07000 NA07037 NA07051 NA07346 NA07347 NA07357 NA10847 NA10851 NA11829 NA11830 NA11831 NA11832 NA11840 NA11881 NA11894 NA11918 NA11919 NA11920 NA11931 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12005 NA12006 NA12043 NA12044 NA12045 NA12144 NA12154 NA12155 NA12156 NA12234 NA12249 NA12287 NA12414 NA12489 NA12716 NA12717 NA12749 NA12750 NA12751 NA12760 NA12761 NA12762 NA12763 NA12776 NA12812 NA12813 NA12814 NA12815 NA12828 NA12872 NA12873 NA12874 NA12878 NA12891 NA12892
1 17786644 rs34417109 G A 60.0 PASS NS=60;DP=279;AN=126;AC=6;AA=G;DB=1 GT:GQ:DP:HQ 0|0:90:1:93,93 0|0:84:13:88,85 0|0:90:3:93,93 0|0:90:11:93,93 0|0:9:4:9,93 0|0:90:5:93,93 0|0:90:2:93,93 1|0:44:2:44,88 0|0:90:7:93,93 0/0:52:3 1/0:49:13 0|0:90:3:93,93 0|0:87:2:93,87 0|0:4:0:4,57 0|0:26:2:26,73 0|0:90:7:93,93 0|0:90:4:93,93 0|0:90:2:93,93 0|0:57:1:93,57 0|0:46:3:93,46 0|0:90:18:93,93 0|0:90:5:93,93 0|1:48:9:65,48 0|0:90:2:93,93 0|0:90:3:93,93 0|0:90:5:93,93 0|0:43:8:93,43 0/0:60:2 0|0:90:9:93,93 0|0:37:6:37,93 0|0:90:1:93,93 0|0:90:3:93,93 0|0:90:4:93,93 0|0:46:4:93,46 0|0:90:3:93,93 0|0:90:2:93,93 0|0:90:5:93,93 0|0:90:1:93,93 0|0:87:6:88,93 0|0:83:3:83,93 0/0:37:6 0|0:90:6:93,93 0|0:90:5:93,93 0/0:93:1 0|0:90:16:93,93 0|0:90:3:93,93 0|0:57:8:57,93 0|1:49:3:65,49 0|0:90:4:93,93 0|0:90:2:93,93 0|0:90:5:93,93 0|1:42:2:46,44 0|0:90:4:93,93 0|0:90:2:93,93 0|0:26:5:93,26 0|0:90:2:93,93 1|0:4:4:4,93 0|0:90:7:93,93 0|0:90:2:93,93 0|0:66:2:66,93 0/0:60:0 0|0:4:0:57,4 0|0:90:3:93,93

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public/testdata/ROD_validation/newerTribbleTrack.vcf vendored
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@ -1,7 +0,0 @@
##fileformat=VCFv4.0
##fileDate=20090908
##source=QCALLv1.0
##reference=1000GenomesPilot-NCBI36
##phasing=partial
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA06985 NA06986 NA06994 NA07000 NA07037 NA07051 NA07346 NA07347 NA07357 NA10847 NA10851 NA11829 NA11830 NA11831 NA11832 NA11840 NA11881 NA11894 NA11918 NA11919 NA11920 NA11931 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12005 NA12006 NA12043 NA12044 NA12045 NA12144 NA12154 NA12155 NA12156 NA12234 NA12249 NA12287 NA12414 NA12489 NA12716 NA12717 NA12749 NA12750 NA12751 NA12760 NA12761 NA12762 NA12763 NA12776 NA12812 NA12813 NA12814 NA12815 NA12828 NA12872 NA12873 NA12874 NA12878 NA12891 NA12892
1 17786644 rs34417109 G A 60.0 PASS NS=60;DP=279;AN=126;AC=6;AA=G;DB=1 GT:GQ:DP:HQ 0|0:90:1:93,93 0|0:84:13:88,85 0|0:90:3:93,93 0|0:90:11:93,93 0|0:9:4:9,93 0|0:90:5:93,93 0|0:90:2:93,93 1|0:44:2:44,88 0|0:90:7:93,93 0/0:52:3 1/0:49:13 0|0:90:3:93,93 0|0:87:2:93,87 0|0:4:0:4,57 0|0:26:2:26,73 0|0:90:7:93,93 0|0:90:4:93,93 0|0:90:2:93,93 0|0:57:1:93,57 0|0:46:3:93,46 0|0:90:18:93,93 0|0:90:5:93,93 0|1:48:9:65,48 0|0:90:2:93,93 0|0:90:3:93,93 0|0:90:5:93,93 0|0:43:8:93,43 0/0:60:2 0|0:90:9:93,93 0|0:37:6:37,93 0|0:90:1:93,93 0|0:90:3:93,93 0|0:90:4:93,93 0|0:46:4:93,46 0|0:90:3:93,93 0|0:90:2:93,93 0|0:90:5:93,93 0|0:90:1:93,93 0|0:87:6:88,93 0|0:83:3:83,93 0/0:37:6 0|0:90:6:93,93 0|0:90:5:93,93 0/0:93:1 0|0:90:16:93,93 0|0:90:3:93,93 0|0:57:8:57,93 0|1:49:3:65,49 0|0:90:4:93,93 0|0:90:2:93,93 0|0:90:5:93,93 0|1:42:2:46,44 0|0:90:4:93,93 0|0:90:2:93,93 0|0:26:5:93,26 0|0:90:2:93,93 1|0:4:4:4,93 0|0:90:7:93,93 0|0:90:2:93,93 0|0:66:2:66,93 0/0:60:0 0|0:4:0:57,4 0|0:90:3:93,93

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public/testdata/ROD_validation/read_only/good_index.vcf vendored
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@ -1,7 +0,0 @@
##format=VCRv3.2
##fileDate=20090908
##source=QCALLv1.0
##reference=1000GenomesPilot-NCBI36
##phasing=partial
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA06985 NA06986 NA06994 NA07000 NA07037 NA07051 NA07346 NA07347 NA07357 NA10847 NA10851 NA11829 NA11830 NA11831 NA11832 NA11840 NA11881 NA11894 NA11918 NA11919 NA11920 NA11931 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12005 NA12006 NA12043 NA12044 NA12045 NA12144 NA12154 NA12155 NA12156 NA12234 NA12249 NA12287 NA12414 NA12489 NA12716 NA12717 NA12749 NA12750 NA12751 NA12760 NA12761 NA12762 NA12763 NA12776 NA12812 NA12813 NA12814 NA12815 NA12828 NA12872 NA12873 NA12874 NA12878 NA12891 NA12892
1 17786644 rs34417109 G A 60.0 0 NS=60;DP=279;AN=126;AC=6;AA=G;DB=1 GT:GQ:DP:HQ 0|0:90:1:93,93 0|0:84:13:88,85 0|0:90:3:93,93 0|0:90:11:93,93 0|0:9:4:9,93 0|0:90:5:93,93 0|0:90:2:93,93 1|0:44:2:44,88 0|0:90:7:93,93 0/0:52:3 1/0:49:13 0|0:90:3:93,93 0|0:87:2:93,87 0|0:4:0:4,57 0|0:26:2:26,73 0|0:90:7:93,93 0|0:90:4:93,93 0|0:90:2:93,93 0|0:57:1:93,57 0|0:46:3:93,46 0|0:90:18:93,93 0|0:90:5:93,93 0|1:48:9:65,48 0|0:90:2:93,93 0|0:90:3:93,93 0|0:90:5:93,93 0|0:43:8:93,43 0/0:60:2 0|0:90:9:93,93 0|0:37:6:37,93 0|0:90:1:93,93 0|0:90:3:93,93 0|0:90:4:93,93 0|0:46:4:93,46 0|0:90:3:93,93 0|0:90:2:93,93 0|0:90:5:93,93 0|0:90:1:93,93 0|0:87:6:88,93 0|0:83:3:83,93 0/0:37:6 0|0:90:6:93,93 0|0:90:5:93,93 0/0:93:1 0|0:90:16:93,93 0|0:90:3:93,93 0|0:57:8:57,93 0|1:49:3:65,49 0|0:90:4:93,93 0|0:90:2:93,93 0|0:90:5:93,93 0|1:42:2:46,44 0|0:90:4:93,93 0|0:90:2:93,93 0|0:26:5:93,26 0|0:90:2:93,93 1|0:4:4:4,93 0|0:90:7:93,93 0|0:90:2:93,93 0|0:66:2:66,93 0/0:60:0 0|0:4:0:57,4 0|0:90:3:93,93

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public/testdata/ROD_validation/read_only/no_index.vcf vendored
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@ -1,7 +0,0 @@
##format=VCRv3.2
##fileDate=20090908
##source=QCALLv1.0
##reference=1000GenomesPilot-NCBI36
##phasing=partial
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA06985 NA06986 NA06994 NA07000 NA07037 NA07051 NA07346 NA07347 NA07357 NA10847 NA10851 NA11829 NA11830 NA11831 NA11832 NA11840 NA11881 NA11894 NA11918 NA11919 NA11920 NA11931 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12005 NA12006 NA12043 NA12044 NA12045 NA12144 NA12154 NA12155 NA12156 NA12234 NA12249 NA12287 NA12414 NA12489 NA12716 NA12717 NA12749 NA12750 NA12751 NA12760 NA12761 NA12762 NA12763 NA12776 NA12812 NA12813 NA12814 NA12815 NA12828 NA12872 NA12873 NA12874 NA12878 NA12891 NA12892
1 17786644 rs34417109 G A 60.0 0 NS=60;DP=279;AN=126;AC=6;AA=G;DB=1 GT:GQ:DP:HQ 0|0:90:1:93,93 0|0:84:13:88,85 0|0:90:3:93,93 0|0:90:11:93,93 0|0:9:4:9,93 0|0:90:5:93,93 0|0:90:2:93,93 1|0:44:2:44,88 0|0:90:7:93,93 0/0:52:3 1/0:49:13 0|0:90:3:93,93 0|0:87:2:93,87 0|0:4:0:4,57 0|0:26:2:26,73 0|0:90:7:93,93 0|0:90:4:93,93 0|0:90:2:93,93 0|0:57:1:93,57 0|0:46:3:93,46 0|0:90:18:93,93 0|0:90:5:93,93 0|1:48:9:65,48 0|0:90:2:93,93 0|0:90:3:93,93 0|0:90:5:93,93 0|0:43:8:93,43 0/0:60:2 0|0:90:9:93,93 0|0:37:6:37,93 0|0:90:1:93,93 0|0:90:3:93,93 0|0:90:4:93,93 0|0:46:4:93,46 0|0:90:3:93,93 0|0:90:2:93,93 0|0:90:5:93,93 0|0:90:1:93,93 0|0:87:6:88,93 0|0:83:3:83,93 0/0:37:6 0|0:90:6:93,93 0|0:90:5:93,93 0/0:93:1 0|0:90:16:93,93 0|0:90:3:93,93 0|0:57:8:57,93 0|1:49:3:65,49 0|0:90:4:93,93 0|0:90:2:93,93 0|0:90:5:93,93 0|1:42:2:46,44 0|0:90:4:93,93 0|0:90:2:93,93 0|0:26:5:93,26 0|0:90:2:93,93 1|0:4:4:4,93 0|0:90:7:93,93 0|0:90:2:93,93 0|0:66:2:66,93 0/0:60:0 0|0:4:0:57,4 0|0:90:3:93,93

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public/testdata/ROD_validation/read_only/relic.vcf vendored
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@ -1,7 +0,0 @@
##format=VCRv3.2
##fileDate=20090908
##source=QCALLv1.0
##reference=1000GenomesPilot-NCBI36
##phasing=partial
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA06985 NA06986 NA06994 NA07000 NA07037 NA07051 NA07346 NA07347 NA07357 NA10847 NA10851 NA11829 NA11830 NA11831 NA11832 NA11840 NA11881 NA11894 NA11918 NA11919 NA11920 NA11931 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12005 NA12006 NA12043 NA12044 NA12045 NA12144 NA12154 NA12155 NA12156 NA12234 NA12249 NA12287 NA12414 NA12489 NA12716 NA12717 NA12749 NA12750 NA12751 NA12760 NA12761 NA12762 NA12763 NA12776 NA12812 NA12813 NA12814 NA12815 NA12828 NA12872 NA12873 NA12874 NA12878 NA12891 NA12892
1 17786644 rs34417109 G A 60.0 0 NS=60;DP=279;AN=126;AC=6;AA=G;DB=1 GT:GQ:DP:HQ 0|0:90:1:93,93 0|0:84:13:88,85 0|0:90:3:93,93 0|0:90:11:93,93 0|0:9:4:9,93 0|0:90:5:93,93 0|0:90:2:93,93 1|0:44:2:44,88 0|0:90:7:93,93 0/0:52:3 1/0:49:13 0|0:90:3:93,93 0|0:87:2:93,87 0|0:4:0:4,57 0|0:26:2:26,73 0|0:90:7:93,93 0|0:90:4:93,93 0|0:90:2:93,93 0|0:57:1:93,57 0|0:46:3:93,46 0|0:90:18:93,93 0|0:90:5:93,93 0|1:48:9:65,48 0|0:90:2:93,93 0|0:90:3:93,93 0|0:90:5:93,93 0|0:43:8:93,43 0/0:60:2 0|0:90:9:93,93 0|0:37:6:37,93 0|0:90:1:93,93 0|0:90:3:93,93 0|0:90:4:93,93 0|0:46:4:93,46 0|0:90:3:93,93 0|0:90:2:93,93 0|0:90:5:93,93 0|0:90:1:93,93 0|0:87:6:88,93 0|0:83:3:83,93 0/0:37:6 0|0:90:6:93,93 0|0:90:5:93,93 0/0:93:1 0|0:90:16:93,93 0|0:90:3:93,93 0|0:57:8:57,93 0|1:49:3:65,49 0|0:90:4:93,93 0|0:90:2:93,93 0|0:90:5:93,93 0|1:42:2:46,44 0|0:90:4:93,93 0|0:90:2:93,93 0|0:26:5:93,26 0|0:90:2:93,93 1|0:4:4:4,93 0|0:90:7:93,93 0|0:90:2:93,93 0|0:66:2:66,93 0/0:60:0 0|0:4:0:57,4 0|0:90:3:93,93

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public/testdata/complexExample.vcf4 vendored 100644
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@ -0,0 +1,23 @@
##fileformat=VCFv4.0
##source=ArbitrarySource
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##reference=human_b36_both.fasta
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
1 10001292 testid1 G A 12.22 PASS AF=0.50;AlleleBalance=0.57;DoC=23;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=46.31;SB=-24.92;SpanningDeletions=0 GT:DP:GQ 1/0:23:19.27 ./. ./.
1 10002963 . C G 22.22 . AF=0.50;AlleleBalance=0.47;DoC=30;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.91;SB=-41.73;SpanningDeletions=0 GT:DP:GQ 0/1:30:33.07 ./. ./.
1 10005008 . A T,C 123.78 PASS AF=1.00;DoC=30;HomopolymerRun=6;MAPQ0=2;NS=1;RMSMAPQ=61.05;SB=-75.45;SpanningDeletions=1 GT:DP:GQ 1/1:27:4.03 0/1:26:3.0 0/0:16:2.0
1 10006296 . C T 42.23 PASS AF=0.50;AlleleBalance=0.33;DoC=7;HomopolymerRun=0;MAPQ0=11;NS=1;RMSMAPQ=46.62;SB=-0.04;SpanningDeletions=0 GT:DP:GQ 0/1:7:2000000 ./. ./.
1 10023478 . G C,A,T 84.23 . AF=1.00;DoC=27;HomopolymerRun=1;MAPQ0=10;NS=1;RMSMAPQ=42.16;SB=-48.38;SpanningDeletions=0 GT:DP:GQ 1/1:27:4.03 2/2:26:3.0 0/3:16:2.0
1 10029362 . T C 52.22 . AF=0.50;AlleleBalance=0.52;DoC=44;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.28;SB=-42.22;SpanningDeletions=0 GT:DP:GQ ./. 1/0:-1:36.62 ./.
1 10042312 . G C 31.81 . AF=0.50;AlleleBalance=0.70;DoC=24;HomopolymerRun=1;MAPQ0=0;NS=1;RMSMAPQ=85.07;SB=0.00;SpanningDeletions=0 GT:DP:GQ 1/0:.:5.85 0/0 0/1:4
1 10044557 . C T 62.22 . AF=0.50;AlleleBalance=0.68;DoC=31;HomopolymerRun=16;MAPQ0=0;NS=1;RMSMAPQ=85.34;SB=-0.00;SpanningDeletions=0 GT:DP:GQ ./. ./. 0/1:31:15.01
1 10045603 . AAAA A 40.26 PASS AF=0.50 GT:DP:GQ 0/1:15:7.94 0/0:15:7.94 1/1:15:7.94
1 10045604 . A ACAT 41.26 PASS AF=0.50 GT:DP:GQ 1/1:14:6.94 0/0:15:7.94 1/0:15:7.94
1 10048142 . A G 126.81 foo AF=1.00;DoC=36;HomopolymerRun=4;MAPQ0=0;NS=1;RMSMAPQ=82.11;SB=-85.45;SpanningDeletions=0 GT:DP:GQ 0/1:15:7.94 0/0:15:7.94 1/1:15:7.94
1 10048580 . T A 72.22 bar;baz AF=0.50;AlleleBalance=0.69;DoC=33;HomopolymerRun=6;MAPQ0=0;NS=1;RMSMAPQ=84.45;SB=-27.41;SpanningDeletions=0 GT:DP:GQ 0/1:15:7.94 0/0:15:7.94 1/1:15:7.94

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