| Next changeset 1:d3f4f86a18d4 (2015-11-11) |
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Commit message:
Uploaded |
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added:
macros.xml test-data/vcflib-test-genome-phix.fa test-data/vcfvcfintersect-input1.vcf test-data/vcfvcfintersect-input2.vcf test-data/vcfvcfintersect-test1.vcf test-data/vcfvcfintersect-test2.vcf tool-data/fasta_indexes.loc.sample tool-data/tool_data_table_conf.xml.sample tool_dependencies.xml vcfvcfintersect.xml |
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| diff -r 000000000000 -r b29dbe1270b5 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 19 14:47:59 2015 -0400 |
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| @@ -0,0 +1,28 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="8a5602bf07">vcflib</requirement> + <yield/> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> +@misc{Garrison2015, + author = {Garrison, Erik}, + year = {2015}, + title = {vcflib}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ekg/vcflib}, +} + </citation> + </citations> + </xml> + <token name="@IS_PART_OF_VCFLIB@">is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).</token> +</macros> |
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| diff -r 000000000000 -r b29dbe1270b5 test-data/vcflib-test-genome-phix.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcflib-test-genome-phix.fa Thu Mar 19 14:47:59 2015 -0400 |
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| @@ -0,0 +1,2 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA 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| diff -r 000000000000 -r b29dbe1270b5 test-data/vcfvcfintersect-input1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfvcfintersect-input1.vcf Thu Mar 19 14:47:59 2015 -0400 |
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| b'@@ -0,0 +1,121 @@\n+##fileformat=VCFv4.1\n+##fileDate=20140610\n+##source=Dan\n+##reference=file:///galaxy/data/phiX/sam_index/phiX.fa\n+##filter="AF > .001"\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tgroupA\tgroupB\n+phiX174\t1015\t.\tA\tC\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:0,2:0,0.2:A=8,C=2,G=1,\t0:0,0:0,0:A=26,G=1,\n+phiX174\t1016\t.\tA\tT\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:0:0:A=10,\t0:2:0.0769230769231:A=24,T=2,\n+phiX174\t1038\t.\tA\tC\t0\t.\tAC=2;AF=0.046511627907\tGT:AC:AF:NC\t0:2:0.153846153846:A=11,C=2,\t0:0:0:A=30,\n+phiX174\t1045\t.\tT\tG\t0\t.\tAC=2;AF=0.0425531914894\tGT:AC:AF:NC\t0:0:0:T=15,G=1,\t0:2:0.0625:T=30,G=2,\n+phiX174\t1048\t.\tC\tA\t0\t.\tAC=2;AF=0.0434782608696\tGT:AC:AF:NC\t0:2:0.133333333333:A=2,C=13,\t0:0:0:C=31,G=1,\n+phiX174\t1050\t.\tA\tC\t0\t.\tAC=3;AF=0.0714285714286\tGT:AC:AF:NC\t0:0:0:A=12,\t0:3:0.1:A=27,C=3,\n+phiX174\t1051\t.\tT\tG\t0\t.\tAC=2;AF=0.0487804878049\tGT:AC:AF:NC\t0:2:0.166666666667:C=1,T=10,G=2,\t0:0:0:T=29,G=1,\n+phiX174\t1054\t.\tT\tG\t0\t.\tAC=2;AF=0.0454545454545\tGT:AC:AF:NC\t0:2:0.153846153846:T=11,G=2,\t0:0:0:T=31,G=1,\n+phiX174\t1076\t.\tG\tC\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=2,G=17,\t0:0:0:G=36,\n+phiX174\t1080\t.\tG\tC\t0\t.\tAC=2;AF=0.0344827586207\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=2,T=1,G=17,\t0:0:0:C=1,G=39,\n+phiX174\t1092\t.\tT\tG\t0\t.\tAC=2;AF=0.0263157894737\tGT:AC:AF:NC\t0:2:0.0833333333333:C=1,T=22,G=2,\t0:0:0:T=52,G=1,\n+phiX174\t1093\t.\tT\tG\t0\t.\tAC=2;AF=0.025974025974\tGT:AC:AF:NC\t0:2:0.08:T=23,G=2,\t0:0:0:T=52,\n+phiX174\t1102\t.\tT\tC\t0\t.\tAC=6;AF=0.0779220779221\tGT:AC:AF:NC\t0:2:0.0869565217391:C=2,T=21,\t0:4:0.0740740740741:C=4,T=50,\n+phiX174\t1107\t.\tT\tG\t0\t.\tAC=2;AF=0.0277777777778\tGT:AC:AF:NC\t0:0:0:T=22,G=1,\t0:2:0.04:T=48,G=2,\n+phiX174\t1110\t.\tT\tC\t0\t.\tAC=2;AF=0.0277777777778\tGT:AC:AF:NC\t0:2:0.125:C=2,T=14,\t0:0:0:C=1,T=56,G=1,\n+phiX174\t1121\t.\tT\tG\t0\t.\tAC=3;AF=0.041095890411\tGT:AC:AF:NC\t0:0:0:T=19,\t0:3:0.0555555555556:T=51,G=3,\n+phiX174\t1124\t.\tT\tC\t0\t.\tAC=2;AF=0.0307692307692\tGT:AC:AF:NC\t0:0,2:0,0.117647058824:C=2,T=15,G=1,\t0:0,0:0,0:T=48,G=1,\n+phiX174\t1125\t.\tT\tG\t0\t.\tAC=3;AF=0.0454545454545\tGT:AC:AF:NC\t0:3:0.176470588235:T=14,G=3,\t0:0:0:T=49,G=1,\n+phiX174\t1131\t.\tT\tG\t0\t.\tAC=2;AF=0.025641025641\tGT:AC:AF:NC\t0:2:0.0952380952381:T=19,G=2,\t0:0:0:T=57,\n+phiX174\t1141\t.\tT\tG\t0\t.\tAC=2;AF=0.0253164556962\tGT:AC:AF:NC\t0:0:0:T=20,G=1,\t0:2:0.0338983050847:T=57,G=2,\n+phiX174\t1145\t.\tG\tC\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:2:0.0952380952381:C=2,G=19,\t0:0:0:G=52,\n+phiX174\t1147\t.\tT\tC\t0\t.\tAC=2;AF=0.0281690140845\tGT:AC:AF:NC\t0:2:0.0952380952381:C=2,T=19,\t0:0:0:T=50,\n+phiX174\t1149\t.\tT\tG,C\t0\t.\tAC=2,2;AF=0.027027027027,0.027027027027\tGT:AC:AF:NC\t0:2,2:0.1,0.1:C=2,T=16,G=2,\t0:0,0:0,0:T=54,\n+phiX174\t1156\t.\tT\tG\t0\t.\tAC=2;AF=0.031746031746\tGT:AC:AF:NC\t0:0:0:C=1,T=15,\t0:2:0.0416666666667:T=46,G=2,\n+phiX174\t1159\t.\tT\tC,G\t0\t.\tAC=2,2;AF=0.0298507462687,0.0298507462687\tGT:AC:AF:NC\t0:2,0:0.111111111111,0:C=2,T=16,\t0:0,2:0,0.0408163265306:C=1,T=47,G=2,\n+phiX174\t1164\t.\tT\tG\t0\t.\tAC=4;AF=0.0666666666667\tGT:AC:AF:NC\t0:0:0:C=1,T=16,G=1,\t0:4:0.0909090909091:T=40,G=4,\n+phiX174\t1168\t.\tT\tG\t0\t.\tAC=4;AF=0.0666666666667\tGT:AC:AF:NC\t0:2:0.0952380952381:C=1,T=19,G=2,\t0:2:0.0512820512821:T=37,G=2,\n+phiX174\t1171\t.\tT\tG\t0\t.\tAC=2;AF=0.0327868852459\tGT:AC:AF:NC\t0:2:0.0869565217391:T=21,G=2,\t0:0:0:T=38,G=1,\n+phiX174\t1174\t.\tC\tA\t0\t.\tAC=2;AF=0.0327868852459\tGT:AC:AF:NC\t0:2:0.0869565217391:A=2,C=21,\t0:0:0:A=1,C=38,\n+phiX174\t1178\t.\tG\tC\t0\t.\tAC=2;AF=0.03076923076'..b'7907:C=2,T=41,G=1,\n+phiX174\t1347\t.\tA\tC\t0\t.\tAC=2;AF=0.0243902439024\tGT:AC:AF:NC\t0:2:0.0512820512821:A=37,C=2,G=1,\t0:0:0:A=43,\n+phiX174\t1348\t.\tT\tG\t0\t.\tAC=2;AF=0.0240963855422\tGT:AC:AF:NC\t0:2:0.05:T=38,G=2,\t0:0:0:T=43,\n+phiX174\t1352\t.\tA\tT\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:0:0:A=34,G=1,\t0:2:0.0512820512821:A=37,T=2,\n+phiX174\t1354\t.\tT\tG,A\t0\t.\tAC=2,2;AF=0.027027027027,0.027027027027\tGT:AC:AF:NC\t0:2,0:0.0526315789474,0:T=36,G=2,\t0:0,2:0,0.0555555555556:A=2,T=34,G=1,\n+phiX174\t1359\t.\tT\tG\t0\t.\tAC=3;AF=0.0405405405405\tGT:AC:AF:NC\t0:3:0.0714285714286:T=39,G=3,\t0:0:0:T=32,G=1,\n+phiX174\t1366\t.\tG\tC\t0\t.\tAC=3;AF=0.0428571428571\tGT:AC:AF:NC\t0:3:0.0714285714286:C=3,T=1,G=39,\t0:0:0:G=28,\n+phiX174\t1370\t.\tT\tG\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:0:0:C=1,T=45,G=1,\t0:2:0.0833333333333:A=1,T=22,G=2,\n+phiX174\t1373\t.\tT\tG\t0\t.\tAC=2;AF=0.027027027027\tGT:AC:AF:NC\t0:2:0.0408163265306:T=47,G=2,\t0:0:0:T=25,\n+phiX174\t1380\t.\tG\tC\t0\t.\tAC=2;AF=0.0238095238095\tGT:AC:AF:NC\t0:0,2:0,0.0384615384615:C=2,T=1,G=50,\t0:0,0:0,0:T=1,G=32,\n+phiX174\t1381\t.\tT\tG\t0\t.\tAC=3;AF=0.0361445783133\tGT:AC:AF:NC\t0:3:0.0576923076923:A=1,T=49,G=3,\t0:0:0:T=31,\n+phiX174\t1384\t.\tT\tG\t0\t.\tAC=4;AF=0.0512820512821\tGT:AC:AF:NC\t0:4:0.0816326530612:T=45,G=4,\t0:0:0:T=29,G=1,\n+phiX174\t1385\t.\tT\tG\t0\t.\tAC=4;AF=0.0512820512821\tGT:AC:AF:NC\t0:4:0.0816326530612:T=45,G=4,\t0:0:0:C=1,T=29,\n+phiX174\t1391\t.\tA\tC\t0\t.\tAC=2;AF=0.0253164556962\tGT:AC:AF:NC\t0:2:0.0408163265306:A=47,C=2,\t0:0:0:A=30,C=1,\n+phiX174\t1393\t.\tC\tA\t0\t.\tAC=2;AF=0.0253164556962\tGT:AC:AF:NC\t0:2:0.0425531914894:A=2,C=45,\t0:0:0:C=32,\n+phiX174\t1396\t.\tT\tG\t0\t.\tAC=3;AF=0.04\tGT:AC:AF:NC\t0:3:0.0697674418605:T=40,G=3,\t0:0:0:T=32,\n+phiX174\t1397\t.\tA\tC\t0\t.\tAC=2;AF=0.027027027027\tGT:AC:AF:NC\t0:0:0:A=42,T=1,\t0:2:0.0625:A=30,C=2,\n+phiX174\t1400\t.\tA\tC\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:2:0.047619047619:A=40,C=2,G=1,\t0:0:0:A=31,\n+phiX174\t1401\t.\tA\tC\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:2:0.047619047619:A=40,C=2,\t0:0:0:A=31,\n+phiX174\t1434\t.\tC\tT\t0\t.\tAC=2;AF=0.0571428571429\tGT:AC:AF:NC\t0:2:0.142857142857:C=12,T=2,\t0:0:0:C=21,\n+phiX174\t1438\t.\tG\tC\t0\t.\tAC=2;AF=0.0526315789474\tGT:AC:AF:NC\t0:0:0:G=15,\t0:2:0.0869565217391:C=2,G=21,\n+phiX174\t1450\t.\tT\tG\t0\t.\tAC=3;AF=0.0789473684211\tGT:AC:AF:NC\t0:3:0.176470588235:A=1,C=1,T=14,G=3,\t0:0:0:T=21,G=1,\n+phiX174\t1459\t.\tT\tG\t0\t.\tAC=3;AF=0.075\tGT:AC:AF:NC\t0:3:0.142857142857:C=1,T=18,G=3,\t0:0:0:T=19,\n+phiX174\t1470\t.\tC\tA\t0\t.\tAC=2;AF=0.0384615384615\tGT:AC:AF:NC\t0:0:0:C=29,\t0:2:0.0869565217391:A=2,C=21,\n+phiX174\t1484\t.\tC\tG\t0\t.\tAC=2;AF=0.0384615384615\tGT:AC:AF:NC\t0:2:0.0740740740741:A=1,C=25,G=2,\t0:0:0:C=25,\n+phiX174\t1487\t.\tT\tG\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.0689655172414:T=27,G=2,\t0:0:0:T=26,\n+phiX174\t1491\t.\tG\tT\t0\t.\tAC=2;AF=0.037037037037\tGT:AC:AF:NC\t0:0:0:T=1,G=26,\t0:2:0.0714285714286:T=2,G=26,\n+phiX174\t1503\t.\tA\tC\t0\t.\tAC=2;AF=0.0454545454545\tGT:AC:AF:NC\t0:0:0:A=20,C=1,\t0:2:0.0833333333333:A=22,C=2,\n+phiX174\t1536\t.\tA\tC\t0\t.\tAC=3;AF=0.0545454545455\tGT:AC:AF:NC\t0:3:0.111111111111:A=24,C=3,\t0:0:0:A=28,C=1,\n+phiX174\t1541\t.\tT\tG\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.0740740740741:T=25,G=2,\t0:0:0:T=28,\n+phiX174\t1553\t.\tA\tG\t0\t.\tAC=2;AF=0.0408163265306\tGT:AC:AF:NC\t0:2:0.0952380952381:A=19,C=1,G=2,\t0:0:0:A=28,\n+phiX174\t1566\t.\tC\tG\t0\t.\tAC=2;AF=0.0307692307692\tGT:AC:AF:NC\t0:0:0:C=30,T=1,\t0:2:0.0571428571429:C=33,G=2,\n+phiX174\t1572\t.\tT\tG\t0\t.\tAC=2;AF=0.03125\tGT:AC:AF:NC\t0:2:0.0625:T=30,G=2,\t0:0:0:T=32,\n+phiX174\t1574\t.\tG\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.0882352941176:C=3,G=31,\t0:0:0:G=34,\n+phiX174\t1575\t.\tA\tC\t0\t.\tAC=2;AF=0.0294117647059\tGT:AC:AF:NC\t0:2:0.0571428571429:A=33,C=2,\t0:0:0:A=33,T=1,\n+phiX174\t1577\t.\tA\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:0:0:A=35,\t0:3:0.0909090909091:A=30,C=3,\n+phiX174\t1581\t.\tT\tG\t0\t.\tAC=2;AF=0.0285714285714\tGT:AC:AF:NC\t0:2:0.0555555555556:C=1,T=34,G=2,\t0:0:0:T=34,G=1,\n+phiX174\t1591\t.\tA\tC\t0\t.\tAC=3;AF=0.037037037037\tGT:AC:AF:NC\t0:3:0.0789473684211:A=35,C=3,\t0:0:0:A=43,C=1,\n+phiX174\t1597\t.\tT\tG\t0\t.\tAC=2;AF=0.025641025641\tGT:AC:AF:NC\t0:2:0.0606060606061:T=31,G=2,\t0:0:0:C=1,T=45,\n' |
| b |
| diff -r 000000000000 -r b29dbe1270b5 test-data/vcfvcfintersect-input2.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfvcfintersect-input2.vcf Thu Mar 19 14:47:59 2015 -0400 |
| b |
| b'@@ -0,0 +1,122 @@\n+##fileformat=VCFv4.1\n+##fileDate=20140610\n+##source=Dan\n+##reference=file:///galaxy/data/phiX/sam_index/phiX.fa\n+##filter="AF > .001"\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tgroupA\tgroupB\n+phiX174\t1503\t.\tA\tC\t0\t.\tAC=2;AF=0.0454545454545\tGT:AC:AF:NC\t0:0:0:A=20,C=1,\t0:2:0.0833333333333:A=22,C=2,\n+phiX174\t1536\t.\tA\tC\t0\t.\tAC=3;AF=0.0545454545455\tGT:AC:AF:NC\t0:3:0.111111111111:A=24,C=3,\t0:0:0:A=28,C=1,\n+phiX174\t1541\t.\tT\tG\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.0740740740741:T=25,G=2,\t0:0:0:T=28,\n+phiX174\t1553\t.\tA\tG\t0\t.\tAC=2;AF=0.0408163265306\tGT:AC:AF:NC\t0:2:0.0952380952381:A=19,C=1,G=2,\t0:0:0:A=28,\n+phiX174\t1566\t.\tC\tG\t0\t.\tAC=2;AF=0.0307692307692\tGT:AC:AF:NC\t0:0:0:C=30,T=1,\t0:2:0.0571428571429:C=33,G=2,\n+phiX174\t1572\t.\tT\tG\t0\t.\tAC=2;AF=0.03125\tGT:AC:AF:NC\t0:2:0.0625:T=30,G=2,\t0:0:0:T=32,\n+phiX174\t1574\t.\tG\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.0882352941176:C=3,G=31,\t0:0:0:G=34,\n+phiX174\t1575\t.\tA\tC\t0\t.\tAC=2;AF=0.0294117647059\tGT:AC:AF:NC\t0:2:0.0571428571429:A=33,C=2,\t0:0:0:A=33,T=1,\n+phiX174\t1577\t.\tA\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:0:0:A=35,\t0:3:0.0909090909091:A=30,C=3,\n+phiX174\t1581\t.\tT\tG\t0\t.\tAC=2;AF=0.0285714285714\tGT:AC:AF:NC\t0:2:0.0555555555556:C=1,T=34,G=2,\t0:0:0:T=34,G=1,\n+phiX174\t1591\t.\tA\tC\t0\t.\tAC=3;AF=0.037037037037\tGT:AC:AF:NC\t0:3:0.0789473684211:A=35,C=3,\t0:0:0:A=43,C=1,\n+phiX174\t1597\t.\tT\tG\t0\t.\tAC=2;AF=0.025641025641\tGT:AC:AF:NC\t0:2:0.0606060606061:T=31,G=2,\t0:0:0:C=1,T=45,\n+phiX174\t1603\t.\tT\tG\t0\t.\tAC=2;AF=0.0243902439024\tGT:AC:AF:NC\t0:2:0.0625:T=30,G=2,\t0:0:0:T=50,\n+phiX174\t1606\t.\tT\tG\t0\t.\tAC=2;AF=0.0243902439024\tGT:AC:AF:NC\t0:2:0.0666666666667:A=1,C=1,T=28,G=2,\t0:0:0:T=52,\n+phiX174\t1611\t.\tA\tC\t0\t.\tAC=2;AF=0.0243902439024\tGT:AC:AF:NC\t0:2:0.0769230769231:A=24,C=2,\t0:0:0:A=56,C=1,\n+phiX174\t1613\t.\tA\tG\t0\t.\tAC=2;AF=0.0240963855422\tGT:AC:AF:NC\t0:0:0:A=25,C=1,G=1,\t0:2:0.0344827586207:A=56,G=2,\n+phiX174\t1618\t.\tC\tA\t0\t.\tAC=2;AF=0.0229885057471\tGT:AC:AF:NC\t0:2:0.0666666666667:A=2,C=28,G=1,\t0:0:0:A=1,C=57,\n+phiX174\t1619\t.\tC\tA\t0\t.\tAC=2;AF=0.0229885057471\tGT:AC:AF:NC\t0:2:0.0666666666667:A=2,C=28,\t0:0:0:C=57,\n+phiX174\t1621\t.\tA\tC\t0\t.\tAC=3;AF=0.0352941176471\tGT:AC:AF:NC\t0:0:0:A=31,T=1,G=1,\t0:3:0.0555555555556:A=51,C=3,\n+phiX174\t1622\t.\tG\tT\t0\t.\tAC=2;AF=0.0224719101124\tGT:AC:AF:NC\t0:0:0:A=1,G=35,\t0:2:0.037037037037:T=2,G=52,\n+phiX174\t1624\t.\tA\tG\t0\t.\tAC=2;AF=0.0235294117647\tGT:AC:AF:NC\t0:2:0.0555555555556:A=34,T=1,G=2,\t0:0:0:A=49,\n+phiX174\t1627\t.\tT\tG,C\t0\t.\tAC=2,2;AF=0.0246913580247,0.0246913580247\tGT:AC:AF:NC\t0:0,0:0,0:T=37,G=1,\t0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2,\n+phiX174\t1630\t.\tT\tG\t0\t.\tAC=2;AF=0.025641025641\tGT:AC:AF:NC\t0:2:0.0526315789474:C=1,T=36,G=2,\t0:0:0:T=40,\n+phiX174\t1632\t.\tA\tC\t0\t.\tAC=2;AF=0.0246913580247\tGT:AC:AF:NC\t0:2:0.05:A=38,C=2,\t0:0:0:A=41,\n+phiX174\t1634\t.\tT\tG\t0\t.\tAC=4;AF=0.0493827160494\tGT:AC:AF:NC\t0:2:0.047619047619:C=1,T=40,G=2,\t0:2:0.0512820512821:T=37,G=2,\n+phiX174\t1635\t.\tT\tG\t0\t.\tAC=3;AF=0.0365853658537\tGT:AC:AF:NC\t0:3:0.0714285714286:T=39,G=3,\t0:0:0:T=40,\n+phiX174\t1639\t.\tG\tA\t0\t.\tAC=3;AF=0.0405405405405\tGT:AC:AF:NC\t0:3:0.075:A=3,T=1,G=37,\t0:0:0:G=34,\n+phiX174\t1645\t.\tT\tG\t0\t.\tAC=2;AF=0.027027027027\tGT:AC:AF:NC\t0:2:0.0425531914894:T=45,G=2,\t0:0:0:T=27,G=1,\n+phiX174\t1647\t.\tA\tT,G,C\t0\t.\tAC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962\tGT:AC:AF:NC\t0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2,\t0:2,0,0:0.0740740740741,0,'..b'\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.0810810810811:A=34,G=3,\t0:0:0:A=31,\n+phiX174\t1775\t.\tG\tA\t0\t.\tAC=2;AF=0.030303030303\tGT:AC:AF:NC\t0:2:0.0571428571429:A=2,G=33,\t0:0:0:G=31,\n+phiX174\t1776\t.\tG\tT\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:2:0.0540540540541:T=2,G=35,\t0:0:0:G=32,\n+phiX174\t1778\t.\tC\tG\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:2:0.0526315789474:C=36,G=2,\t0:0:0:C=31,\n+phiX174\t1779\t.\tA\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.075:A=37,C=3,\t0:0:0:A=28,\n+phiX174\t1781\t.\tT\tG\t0\t.\tAC=5;AF=0.0714285714286\tGT:AC:AF:NC\t0:2:0.0487804878049:C=1,T=39,G=2,\t0:3:0.103448275862:T=26,G=3,\n+phiX174\t1782\t.\tT\tG\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.075:T=37,G=3,\t0:0:0:A=1,T=28,\n+phiX174\t1783\t.\tT\tC\t0\t.\tAC=2;AF=0.0298507462687\tGT:AC:AF:NC\t0:2:0.0512820512821:C=2,T=37,\t0:0:0:T=28,G=1,\n+phiX174\t1788\t.\tG\tT\t0\t.\tAC=2;AF=0.0344827586207\tGT:AC:AF:NC\t0:0:0:A=1,T=1,G=29,\t0:2:0.0689655172414:T=2,G=27,\n+phiX174\t1792\t.\tT\tG\t0\t.\tAC=2;AF=0.0344827586207\tGT:AC:AF:NC\t0:2:0.0606060606061:T=31,G=2,\t0:0:0:T=25,G=1,\n+phiX174\t1802\t.\tA\tC\t0\t.\tAC=2;AF=0.030303030303\tGT:AC:AF:NC\t0:2:0.0571428571429:A=33,C=2,\t0:0:0:A=31,C=1,\n+phiX174\t1804\t.\tC\tT\t0\t.\tAC=2;AF=0.0294117647059\tGT:AC:AF:NC\t0:2:0.0588235294118:A=1,C=32,T=2,\t0:0:0:C=34,\n+phiX174\t1805\t.\tT\tG\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.0857142857143:T=32,G=3,\t0:0:0:T=33,G=1,\n+phiX174\t1806\t.\tA\tC\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:2:0.0571428571429:A=33,C=2,\t0:0:0:A=34,G=1,\n+phiX174\t1824\t.\tG\tC\t0\t.\tAC=2;AF=0.0281690140845\tGT:AC:AF:NC\t0:2:0.0714285714286:C=2,T=1,G=26,\t0:0:0:G=43,\n+phiX174\t1825\t.\tT\tG\t0\t.\tAC=2;AF=0.0281690140845\tGT:AC:AF:NC\t0:2:0.0689655172414:T=27,G=2,\t0:0:0:T=42,G=1,\n+phiX174\t1833\t.\tT\tG\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:0:0:A=1,T=24,\t0:2:0.0444444444444:T=43,G=2,\n+phiX174\t1843\t.\tT\tG\t0\t.\tAC=2;AF=0.031746031746\tGT:AC:AF:NC\t0:2:0.08:A=1,T=23,G=2,\t0:0:0:T=38,\n+phiX174\t1847\t.\tA\tC\t0\t.\tAC=2;AF=0.0333333333333\tGT:AC:AF:NC\t0:2:0.0833333333333:A=22,C=2,T=1,G=1,\t0:0:0:A=36,\n+phiX174\t1854\t.\tT\tG\t0\t.\tAC=2;AF=0.0298507462687\tGT:AC:AF:NC\t0:0:0:T=26,\t0:2:0.0487804878049:T=39,G=2,\n+phiX174\t1860\t.\tT\tG\t0\t.\tAC=2;AF=0.0377358490566\tGT:AC:AF:NC\t0:0:0:A=1,T=20,\t0:2:0.0606060606061:T=31,G=2,\n+phiX174\t1863\t.\tC\tG\t0\t.\tAC=2;AF=0.0384615384615\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=17,G=2,\t0:0:0:C=33,\n+phiX174\t1866\t.\tT\tG\t0\t.\tAC=2;AF=0.04\tGT:AC:AF:NC\t0:0:0:T=19,G=1,\t0:2:0.0645161290323:T=29,G=2,\n+phiX174\t1875\t.\tT\tA\t0\t.\tAC=2;AF=0.0377358490566\tGT:AC:AF:NC\t0:2:0.0952380952381:A=2,T=19,\t0:0:0:T=32,G=1,\n+phiX174\t1876\t.\tT\tG\t0\t.\tAC=3;AF=0.0588235294118\tGT:AC:AF:NC\t0:3:0.157894736842:C=1,T=16,G=3,\t0:0:0:T=32,G=1,\n+phiX174\t1882\t.\tT\tG\t0\t.\tAC=2;AF=0.0377358490566\tGT:AC:AF:NC\t0:2:0.105263157895:T=17,G=2,\t0:0:0:T=34,\n+phiX174\t1889\t.\tA\tC\t0\t.\tAC=2;AF=0.04\tGT:AC:AF:NC\t0:2:0.0869565217391:A=21,C=2,\t0:0:0:A=27,\n+phiX174\t1913\t.\tG\tC\t0\t.\tAC=2;AF=0.04\tGT:AC:AF:NC\t0:0:0:G=27,\t0:2:0.0869565217391:C=2,G=21,\n+phiX174\t1915\t.\tT\tG\t0\t.\tAC=2;AF=0.0425531914894\tGT:AC:AF:NC\t0:0:0:A=1,T=24,\t0:2:0.0869565217391:T=21,G=2,\n+phiX174\t1917\t.\tA\tT\t0\t.\tAC=2;AF=0.0444444444444\tGT:AC:AF:NC\t0:2,0:0.0833333333333,0:A=22,T=2,G=1,\t0:0,0:0,0:A=21,G=1,\n+phiX174\t1930\t.\tT\tA\t0\t.\tAC=2;AF=0.0526315789474\tGT:AC:AF:NC\t0:2:0.0909090909091:A=2,T=20,\t0:0:0:T=16,\n+phiX174\t1934\t.\tA\tC\t0\t.\tAC=2;AF=0.0512820512821\tGT:AC:AF:NC\t0:2:0.0952380952381:A=19,C=2,T=1,\t0:0:0:A=18,C=1,\n+phiX174\t1940\t.\tA\tC\t0\t.\tAC=2;AF=0.046511627907\tGT:AC:AF:NC\t0:2:0.0952380952381:A=19,C=2,\t0:0:0:A=22,C=1,\n+phiX174\t1942\t.\tT\tG\t0\t.\tAC=2;AF=0.047619047619\tGT:AC:AF:NC\t0:0:0:T=19,\t0:2:0.0869565217391:T=21,G=2,\n+phiX174\t1945\t.\tT\tG\t0\t.\tAC=3;AF=0.0769230769231\tGT:AC:AF:NC\t0:0:0:T=15,G=1,\t0:3:0.125:T=21,G=3,\n+phiX174\t1954\t.\tT\tC\t0\t.\tAC=2;AF=0.0625\tGT:AC:AF:NC\t0:0,0:0,0:T=12,G=1,\t0:0,2:0,0.1:C=2,T=18,G=1,\n+phiX174\t1959\t.\tT\tG\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:2:0.153846153846:T=11,G=2,\t0:0:0:T=23,\n+phiX174\t1994\t.\tA\tC\t0\t.\tAC=2;AF=0.0512820512821\tGT:AC:AF:NC\t0:2:0.153846153846:A=11,C=2,\t0:0:0:A=26,\n+phiX174\t1998\t.\tA\tG\t0\t.\tAC=2;AF=0.05\tGT:AC:AF:NC\t0:2:0.142857142857:A=12,G=2,\t0:0:0:A=26,\n' |
| b |
| diff -r 000000000000 -r b29dbe1270b5 test-data/vcfvcfintersect-test1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfvcfintersect-test1.vcf Thu Mar 19 14:47:59 2015 -0400 |
| b |
| @@ -0,0 +1,24 @@ +##fileformat=VCFv4.1 +##fileDate=20140610 +##source=Dan +##reference=file:///galaxy/data/phiX/sam_index/phiX.fa +##filter="AF > .001" +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> +##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT groupA groupB +phiX174 1503 . A C 0 . AC=2;AF=0.0454545454545 GT:AC:AF:NC 0:0:0:A=20,C=1, 0:2:0.0833333333333:A=22,C=2, +phiX174 1536 . A C 0 . AC=3;AF=0.0545454545455 GT:AC:AF:NC 0:3:0.111111111111:A=24,C=3, 0:0:0:A=28,C=1, +phiX174 1541 . T G 0 . AC=2;AF=0.0363636363636 GT:AC:AF:NC 0:2:0.0740740740741:T=25,G=2, 0:0:0:T=28, +phiX174 1553 . A G 0 . AC=2;AF=0.0408163265306 GT:AC:AF:NC 0:2:0.0952380952381:A=19,C=1,G=2, 0:0:0:A=28, +phiX174 1566 . C G 0 . AC=2;AF=0.0307692307692 GT:AC:AF:NC 0:0:0:C=30,T=1, 0:2:0.0571428571429:C=33,G=2, +phiX174 1572 . T G 0 . AC=2;AF=0.03125 GT:AC:AF:NC 0:2:0.0625:T=30,G=2, 0:0:0:T=32, +phiX174 1574 . G C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:3:0.0882352941176:C=3,G=31, 0:0:0:G=34, +phiX174 1575 . A C 0 . AC=2;AF=0.0294117647059 GT:AC:AF:NC 0:2:0.0571428571429:A=33,C=2, 0:0:0:A=33,T=1, +phiX174 1577 . A C 0 . AC=3;AF=0.0441176470588 GT:AC:AF:NC 0:0:0:A=35, 0:3:0.0909090909091:A=30,C=3, +phiX174 1581 . T G 0 . AC=2;AF=0.0285714285714 GT:AC:AF:NC 0:2:0.0555555555556:C=1,T=34,G=2, 0:0:0:T=34,G=1, +phiX174 1591 . A C 0 . AC=3;AF=0.037037037037 GT:AC:AF:NC 0:3:0.0789473684211:A=35,C=3, 0:0:0:A=43,C=1, +phiX174 1597 . T G 0 . AC=2;AF=0.025641025641 GT:AC:AF:NC 0:2:0.0606060606061:T=31,G=2, 0:0:0:C=1,T=45, |
| b |
| diff -r 000000000000 -r b29dbe1270b5 test-data/vcfvcfintersect-test2.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfvcfintersect-test2.vcf Thu Mar 19 14:47:59 2015 -0400 |
| b |
| b'@@ -0,0 +1,219 @@\n+##fileformat=VCFv4.1\n+##fileDate=20140610\n+##source=Dan\n+##reference=file:///galaxy/data/phiX/sam_index/phiX.fa\n+##filter="AF > .001"\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\n+##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tgroupA\tgroupB\n+phiX174\t1015\t.\tA\tC\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:0,2:0,0.2:A=8,C=2,G=1,\t0:0,0:0,0:A=26,G=1,\n+phiX174\t1016\t.\tA\tT\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:0:0:A=10,\t0:2:0.0769230769231:A=24,T=2,\n+phiX174\t1038\t.\tA\tC\t0\t.\tAC=2;AF=0.046511627907\tGT:AC:AF:NC\t0:2:0.153846153846:A=11,C=2,\t0:0:0:A=30,\n+phiX174\t1045\t.\tT\tG\t0\t.\tAC=2;AF=0.0425531914894\tGT:AC:AF:NC\t0:0:0:T=15,G=1,\t0:2:0.0625:T=30,G=2,\n+phiX174\t1048\t.\tC\tA\t0\t.\tAC=2;AF=0.0434782608696\tGT:AC:AF:NC\t0:2:0.133333333333:A=2,C=13,\t0:0:0:C=31,G=1,\n+phiX174\t1050\t.\tA\tC\t0\t.\tAC=3;AF=0.0714285714286\tGT:AC:AF:NC\t0:0:0:A=12,\t0:3:0.1:A=27,C=3,\n+phiX174\t1051\t.\tT\tG\t0\t.\tAC=2;AF=0.0487804878049\tGT:AC:AF:NC\t0:2:0.166666666667:C=1,T=10,G=2,\t0:0:0:T=29,G=1,\n+phiX174\t1054\t.\tT\tG\t0\t.\tAC=2;AF=0.0454545454545\tGT:AC:AF:NC\t0:2:0.153846153846:T=11,G=2,\t0:0:0:T=31,G=1,\n+phiX174\t1076\t.\tG\tC\t0\t.\tAC=2;AF=0.0363636363636\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=2,G=17,\t0:0:0:G=36,\n+phiX174\t1080\t.\tG\tC\t0\t.\tAC=2;AF=0.0344827586207\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=2,T=1,G=17,\t0:0:0:C=1,G=39,\n+phiX174\t1092\t.\tT\tG\t0\t.\tAC=2;AF=0.0263157894737\tGT:AC:AF:NC\t0:2:0.0833333333333:C=1,T=22,G=2,\t0:0:0:T=52,G=1,\n+phiX174\t1093\t.\tT\tG\t0\t.\tAC=2;AF=0.025974025974\tGT:AC:AF:NC\t0:2:0.08:T=23,G=2,\t0:0:0:T=52,\n+phiX174\t1102\t.\tT\tC\t0\t.\tAC=6;AF=0.0779220779221\tGT:AC:AF:NC\t0:2:0.0869565217391:C=2,T=21,\t0:4:0.0740740740741:C=4,T=50,\n+phiX174\t1107\t.\tT\tG\t0\t.\tAC=2;AF=0.0277777777778\tGT:AC:AF:NC\t0:0:0:T=22,G=1,\t0:2:0.04:T=48,G=2,\n+phiX174\t1110\t.\tT\tC\t0\t.\tAC=2;AF=0.0277777777778\tGT:AC:AF:NC\t0:2:0.125:C=2,T=14,\t0:0:0:C=1,T=56,G=1,\n+phiX174\t1121\t.\tT\tG\t0\t.\tAC=3;AF=0.041095890411\tGT:AC:AF:NC\t0:0:0:T=19,\t0:3:0.0555555555556:T=51,G=3,\n+phiX174\t1124\t.\tT\tC\t0\t.\tAC=2;AF=0.0307692307692\tGT:AC:AF:NC\t0:0,2:0,0.117647058824:C=2,T=15,G=1,\t0:0,0:0,0:T=48,G=1,\n+phiX174\t1125\t.\tT\tG\t0\t.\tAC=3;AF=0.0454545454545\tGT:AC:AF:NC\t0:3:0.176470588235:T=14,G=3,\t0:0:0:T=49,G=1,\n+phiX174\t1131\t.\tT\tG\t0\t.\tAC=2;AF=0.025641025641\tGT:AC:AF:NC\t0:2:0.0952380952381:T=19,G=2,\t0:0:0:T=57,\n+phiX174\t1141\t.\tT\tG\t0\t.\tAC=2;AF=0.0253164556962\tGT:AC:AF:NC\t0:0:0:T=20,G=1,\t0:2:0.0338983050847:T=57,G=2,\n+phiX174\t1145\t.\tG\tC\t0\t.\tAC=2;AF=0.027397260274\tGT:AC:AF:NC\t0:2:0.0952380952381:C=2,G=19,\t0:0:0:G=52,\n+phiX174\t1147\t.\tT\tC\t0\t.\tAC=2;AF=0.0281690140845\tGT:AC:AF:NC\t0:2:0.0952380952381:C=2,T=19,\t0:0:0:T=50,\n+phiX174\t1149\t.\tT\tG,C\t0\t.\tAC=2,2;AF=0.027027027027,0.027027027027\tGT:AC:AF:NC\t0:2,2:0.1,0.1:C=2,T=16,G=2,\t0:0,0:0,0:T=54,\n+phiX174\t1156\t.\tT\tG\t0\t.\tAC=2;AF=0.031746031746\tGT:AC:AF:NC\t0:0:0:C=1,T=15,\t0:2:0.0416666666667:T=46,G=2,\n+phiX174\t1159\t.\tT\tC,G\t0\t.\tAC=2,2;AF=0.0298507462687,0.0298507462687\tGT:AC:AF:NC\t0:2,0:0.111111111111,0:C=2,T=16,\t0:0,2:0,0.0408163265306:C=1,T=47,G=2,\n+phiX174\t1164\t.\tT\tG\t0\t.\tAC=4;AF=0.0666666666667\tGT:AC:AF:NC\t0:0:0:C=1,T=16,G=1,\t0:4:0.0909090909091:T=40,G=4,\n+phiX174\t1168\t.\tT\tG\t0\t.\tAC=4;AF=0.0666666666667\tGT:AC:AF:NC\t0:2:0.0952380952381:C=1,T=19,G=2,\t0:2:0.0512820512821:T=37,G=2,\n+phiX174\t1171\t.\tT\tG\t0\t.\tAC=2;AF=0.0327868852459\tGT:AC:AF:NC\t0:2:0.0869565217391:T=21,G=2,\t0:0:0:T=38,G=1,\n+phiX174\t1174\t.\tC\tA\t0\t.\tAC=2;AF=0.0327868852459\tGT:AC:AF:NC\t0:2:0.0869565217391:A=2,C=21,\t0:0:0:A=1,C=38,\n+phiX174\t1178\t.\tG\tC\t0\t.\tAC=2;AF=0.03076923076'..b'\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.0810810810811:A=34,G=3,\t0:0:0:A=31,\n+phiX174\t1775\t.\tG\tA\t0\t.\tAC=2;AF=0.030303030303\tGT:AC:AF:NC\t0:2:0.0571428571429:A=2,G=33,\t0:0:0:G=31,\n+phiX174\t1776\t.\tG\tT\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:2:0.0540540540541:T=2,G=35,\t0:0:0:G=32,\n+phiX174\t1778\t.\tC\tG\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:2:0.0526315789474:C=36,G=2,\t0:0:0:C=31,\n+phiX174\t1779\t.\tA\tC\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.075:A=37,C=3,\t0:0:0:A=28,\n+phiX174\t1781\t.\tT\tG\t0\t.\tAC=5;AF=0.0714285714286\tGT:AC:AF:NC\t0:2:0.0487804878049:C=1,T=39,G=2,\t0:3:0.103448275862:T=26,G=3,\n+phiX174\t1782\t.\tT\tG\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.075:T=37,G=3,\t0:0:0:A=1,T=28,\n+phiX174\t1783\t.\tT\tC\t0\t.\tAC=2;AF=0.0298507462687\tGT:AC:AF:NC\t0:2:0.0512820512821:C=2,T=37,\t0:0:0:T=28,G=1,\n+phiX174\t1788\t.\tG\tT\t0\t.\tAC=2;AF=0.0344827586207\tGT:AC:AF:NC\t0:0:0:A=1,T=1,G=29,\t0:2:0.0689655172414:T=2,G=27,\n+phiX174\t1792\t.\tT\tG\t0\t.\tAC=2;AF=0.0344827586207\tGT:AC:AF:NC\t0:2:0.0606060606061:T=31,G=2,\t0:0:0:T=25,G=1,\n+phiX174\t1802\t.\tA\tC\t0\t.\tAC=2;AF=0.030303030303\tGT:AC:AF:NC\t0:2:0.0571428571429:A=33,C=2,\t0:0:0:A=31,C=1,\n+phiX174\t1804\t.\tC\tT\t0\t.\tAC=2;AF=0.0294117647059\tGT:AC:AF:NC\t0:2:0.0588235294118:A=1,C=32,T=2,\t0:0:0:C=34,\n+phiX174\t1805\t.\tT\tG\t0\t.\tAC=3;AF=0.0441176470588\tGT:AC:AF:NC\t0:3:0.0857142857143:T=32,G=3,\t0:0:0:T=33,G=1,\n+phiX174\t1806\t.\tA\tC\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:2:0.0571428571429:A=33,C=2,\t0:0:0:A=34,G=1,\n+phiX174\t1824\t.\tG\tC\t0\t.\tAC=2;AF=0.0281690140845\tGT:AC:AF:NC\t0:2:0.0714285714286:C=2,T=1,G=26,\t0:0:0:G=43,\n+phiX174\t1825\t.\tT\tG\t0\t.\tAC=2;AF=0.0281690140845\tGT:AC:AF:NC\t0:2:0.0689655172414:T=27,G=2,\t0:0:0:T=42,G=1,\n+phiX174\t1833\t.\tT\tG\t0\t.\tAC=2;AF=0.0289855072464\tGT:AC:AF:NC\t0:0:0:A=1,T=24,\t0:2:0.0444444444444:T=43,G=2,\n+phiX174\t1843\t.\tT\tG\t0\t.\tAC=2;AF=0.031746031746\tGT:AC:AF:NC\t0:2:0.08:A=1,T=23,G=2,\t0:0:0:T=38,\n+phiX174\t1847\t.\tA\tC\t0\t.\tAC=2;AF=0.0333333333333\tGT:AC:AF:NC\t0:2:0.0833333333333:A=22,C=2,T=1,G=1,\t0:0:0:A=36,\n+phiX174\t1854\t.\tT\tG\t0\t.\tAC=2;AF=0.0298507462687\tGT:AC:AF:NC\t0:0:0:T=26,\t0:2:0.0487804878049:T=39,G=2,\n+phiX174\t1860\t.\tT\tG\t0\t.\tAC=2;AF=0.0377358490566\tGT:AC:AF:NC\t0:0:0:A=1,T=20,\t0:2:0.0606060606061:T=31,G=2,\n+phiX174\t1863\t.\tC\tG\t0\t.\tAC=2;AF=0.0384615384615\tGT:AC:AF:NC\t0:2:0.105263157895:A=1,C=17,G=2,\t0:0:0:C=33,\n+phiX174\t1866\t.\tT\tG\t0\t.\tAC=2;AF=0.04\tGT:AC:AF:NC\t0:0:0:T=19,G=1,\t0:2:0.0645161290323:T=29,G=2,\n+phiX174\t1875\t.\tT\tA\t0\t.\tAC=2;AF=0.0377358490566\tGT:AC:AF:NC\t0:2:0.0952380952381:A=2,T=19,\t0:0:0:T=32,G=1,\n+phiX174\t1876\t.\tT\tG\t0\t.\tAC=3;AF=0.0588235294118\tGT:AC:AF:NC\t0:3:0.157894736842:C=1,T=16,G=3,\t0:0:0:T=32,G=1,\n+phiX174\t1882\t.\tT\tG\t0\t.\tAC=2;AF=0.0377358490566\tGT:AC:AF:NC\t0:2:0.105263157895:T=17,G=2,\t0:0:0:T=34,\n+phiX174\t1889\t.\tA\tC\t0\t.\tAC=2;AF=0.04\tGT:AC:AF:NC\t0:2:0.0869565217391:A=21,C=2,\t0:0:0:A=27,\n+phiX174\t1913\t.\tG\tC\t0\t.\tAC=2;AF=0.04\tGT:AC:AF:NC\t0:0:0:G=27,\t0:2:0.0869565217391:C=2,G=21,\n+phiX174\t1915\t.\tT\tG\t0\t.\tAC=2;AF=0.0425531914894\tGT:AC:AF:NC\t0:0:0:A=1,T=24,\t0:2:0.0869565217391:T=21,G=2,\n+phiX174\t1917\t.\tA\tT\t0\t.\tAC=2;AF=0.0444444444444\tGT:AC:AF:NC\t0:2,0:0.0833333333333,0:A=22,T=2,G=1,\t0:0,0:0,0:A=21,G=1,\n+phiX174\t1930\t.\tT\tA\t0\t.\tAC=2;AF=0.0526315789474\tGT:AC:AF:NC\t0:2:0.0909090909091:A=2,T=20,\t0:0:0:T=16,\n+phiX174\t1934\t.\tA\tC\t0\t.\tAC=2;AF=0.0512820512821\tGT:AC:AF:NC\t0:2:0.0952380952381:A=19,C=2,T=1,\t0:0:0:A=18,C=1,\n+phiX174\t1940\t.\tA\tC\t0\t.\tAC=2;AF=0.046511627907\tGT:AC:AF:NC\t0:2:0.0952380952381:A=19,C=2,\t0:0:0:A=22,C=1,\n+phiX174\t1942\t.\tT\tG\t0\t.\tAC=2;AF=0.047619047619\tGT:AC:AF:NC\t0:0:0:T=19,\t0:2:0.0869565217391:T=21,G=2,\n+phiX174\t1945\t.\tT\tG\t0\t.\tAC=3;AF=0.0769230769231\tGT:AC:AF:NC\t0:0:0:T=15,G=1,\t0:3:0.125:T=21,G=3,\n+phiX174\t1954\t.\tT\tC\t0\t.\tAC=2;AF=0.0625\tGT:AC:AF:NC\t0:0,0:0,0:T=12,G=1,\t0:0,2:0,0.1:C=2,T=18,G=1,\n+phiX174\t1959\t.\tT\tG\t0\t.\tAC=2;AF=0.0555555555556\tGT:AC:AF:NC\t0:2:0.153846153846:T=11,G=2,\t0:0:0:T=23,\n+phiX174\t1994\t.\tA\tC\t0\t.\tAC=2;AF=0.0512820512821\tGT:AC:AF:NC\t0:2:0.153846153846:A=11,C=2,\t0:0:0:A=26,\n+phiX174\t1998\t.\tA\tG\t0\t.\tAC=2;AF=0.05\tGT:AC:AF:NC\t0:2:0.142857142857:A=12,G=2,\t0:0:0:A=26,\n' |
| b |
| diff -r 000000000000 -r b29dbe1270b5 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Thu Mar 19 14:47:59 2015 -0400 |
| b |
| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
| b |
| diff -r 000000000000 -r b29dbe1270b5 tool-data/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Thu Mar 19 14:47:59 2015 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Location of SAMTools indexes and other files --> + <table name="fasta_indexes" comment_char="#"> + <columns>line_type, value, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r b29dbe1270b5 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Mar 19 14:47:59 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="vcflib" version="8a5602bf07"> + <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
| b |
| diff -r 000000000000 -r b29dbe1270b5 vcfvcfintersect.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcfvcfintersect.xml Thu Mar 19 14:47:59 2015 -0400 |
| b |
| @@ -0,0 +1,124 @@ +<tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="0.0.3"> + <description>Intersect two VCF datasets</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <command> + + #set $reference_fasta_filename = "localref.fa" + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + + #if $adv_options.adv_options_selector == True: + + vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" + + #else: + + vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}" + + #end if + + </command> + <inputs> + <!-- selecting refernce source --> + <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" /> + <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset" help="The second dataset will be instersected with the first"/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome" help="This tools needs to access reference genomes sequence specified by this option."> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Select reference genome"> + <options from_data_table="fasta_indexes"> + <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> <!-- FIX ME!!!! --> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + <param name="isect_union" type="select" label="Union or intersection" help="-i or -u"> + <option value="-i">Intersect</option> + <option value="-u">Union</option> + </param> + <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert" /> + <param name="window_size" type="integer" value="30" label="compare records up to this many bp away (window size)" help="-w, --window-size" /> + <param name="loci" type="boolean" truevalue="-l" falsevalue="" label="output whole loci when one alternate allele matches" help="-l, --loci" /> + <conditional name="adv_options"> + <param name="adv_options_selector" type="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/> + <when value="use_adv_controls"> + <param name="adv_options_input" type="text" value="-t "vcfvcf-intersect-result"" label="Enter additional command line options described in the help section below" help="such as -m, -t, -V, -M, and -T" /> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </when> + </conditional> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> + <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> + <param name="isect_union" value="-i" /> + <param name="invert" value="False" /> + <param name="loci" value="False" /> + <patam name="adv_options" value="False" /> + <param name="window_size" value="30" /> + <param name="ref_file" value="vcflib-test-genome-phix.fa" /> + <output name="out_file1" file="vcfvcfintersect-test1.vcf"/> + </test> + <test> + <param name="reference_source_selector" value="history" /> + <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" /> + <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" /> + <param name="isect_union" value="-u" /> + <param name="invert" value="False" /> + <param name="loci" value="False" /> + <patam name="adv_options" value="False" /> + <param name="window_size" value="30" /> + <param name="ref_file" value="vcflib-test-genome-phix.fa" /> + <output name="out_file1" file="vcfvcfintersect-test2.vcf"/> + </test> + </tests> + <help> + +Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp. + +The options are:: + + -v, --invert invert the selection, printing only records which would + -i, --intersect-vcf FILE use this VCF for set intersection generation + -u, --union-vcf FILE use this VCF for set union generation + -w, --window-size N compare records up to this many bp away (default 30) + -l, --loci output whole loci when one alternate allele matches + -m, --ref-match intersect on the basis of record REF string + -t, --tag TAG attach TAG to each record's info field if it would intersect + -V, --tag-value VAL use this value to indicate that the allele is passing + '.' will be used otherwise. default: 'PASS' + -M, --merge-from FROM-TAG + -T, --merge-to TO-TAG merge from FROM-TAG used in the -i file, setting TO-TAG + in the current file. + +---- + +VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). +</help> + <expand macro="citations" /> +</tool> |