├── .gitignore ├── src ├── test │ ├── resources │ │ ├── test_data │ │ │ ├── OUTPUT │ │ │ │ ├── MiscSetOperTests │ │ │ │ │ ├── Compare │ │ │ │ │ │ ├── AcompB.out.vcf │ │ │ │ │ │ ├── BcompA.out.vcf │ │ │ │ │ │ ├── intersect.out.vcf │ │ │ │ │ │ └── union.out.vcf │ │ │ │ │ ├── AddCHR │ │ │ │ │ │ └── O_AcompB.vcf │ │ │ │ │ ├── NoCall │ │ │ │ │ │ └── O_AcompB.vcf │ │ │ │ │ ├── RepairHeader │ │ │ │ │ │ └── O_AcompB.vcf │ │ │ │ │ ├── PrintIntermediate │ │ │ │ │ │ └── inter.out.vcf │ │ │ │ │ └── SamplesWithinSameFile │ │ │ │ │ │ └── O_AcompB.vcf │ │ │ │ ├── union │ │ │ │ │ ├── u_test1_out.vcf.idx │ │ │ │ │ ├── testUniqueSampleSetsDifferentVariantSets.vcf.idx │ │ │ │ │ └── u_test2_out.vcf │ │ │ │ ├── intersect │ │ │ │ │ ├── Alt │ │ │ │ │ │ ├── i_test1_out.vcf.idx │ │ │ │ │ │ └── i_test1_out.vcf │ │ │ │ │ ├── Pos │ │ │ │ │ │ ├── i_test1_out.vcf.idx │ │ │ │ │ │ └── i_test1_out.vcf │ │ │ │ │ ├── Het_Only │ │ │ │ │ │ ├── i_test1_out.vcf.idx │ │ │ │ │ │ └── i_test1_out.vcf │ │ │ │ │ ├── Homo_Alt │ │ │ │ │ │ ├── i_test1_out.vcf.idx │ │ │ │ │ │ └── i_test1_out.vcf │ │ │ │ │ ├── Homo_Ref │ │ │ │ │ │ ├── i_test1_out.vcf.idx │ │ │ │ │ │ └── i_test1_out.vcf │ │ │ │ │ ├── Match_Sample │ │ │ │ │ │ ├── i_test1_out.vcf.idx │ │ │ │ │ │ └── i_test1_out.vcf │ │ │ │ │ └── Het_Or_Homo_Alt │ │ │ │ │ │ ├── i_test1_out.vcf.idx │ │ │ │ │ │ └── i_test1_out.vcf │ │ │ │ └── Complement │ │ │ │ │ ├── Alt │ │ │ │ │ ├── i_test1_out.vcf.idx │ │ │ │ │ └── i_test1_out.vcf │ │ │ │ │ ├── Exact │ │ │ │ │ ├── i_test1_out.vcf.idx │ │ │ │ │ └── i_test1_out.vcf │ │ │ │ │ └── Het_or_Homo_Alt │ │ │ │ │ ├── i_test1_out.vcf.idx │ │ │ │ │ └── i_test1_out.vcf │ │ │ ├── phenos │ │ │ │ ├── pheno3 │ │ │ │ ├── pheno4 │ │ │ │ └── pheno2 │ │ │ ├── TSVC_variants.vcf.gz │ │ │ ├── MiscSetOperTests │ │ │ │ ├── AddCHR │ │ │ │ │ ├── README │ │ │ │ │ ├── input1.vcf │ │ │ │ │ ├── input2.vcf │ │ │ │ │ └── Answer.AcompB.vcf │ │ │ │ ├── NoCall │ │ │ │ │ ├── README │ │ │ │ │ ├── input1.vcf │ │ │ │ │ ├── input2.vcf │ │ │ │ │ ├── Answer.AcompB.vcf │ │ │ │ │ └── Answer.intersect.vcf │ │ │ │ ├── RepairHeader │ │ │ │ │ ├── README │ │ │ │ │ ├── input1.vcf │ │ │ │ │ ├── input2.vcf │ │ │ │ │ └── Answer.AcompB.vcf │ │ │ │ ├── SamplesWithinSameFile │ │ │ │ │ ├── README │ │ │ │ │ ├── input1.vcf │ │ │ │ │ ├── input2.vcf │ │ │ │ │ └── Answer.AcompB.vcf │ │ │ │ ├── PrintIntermediate │ │ │ │ │ ├── README │ │ │ │ │ ├── Answer.intersect.vcf │ │ │ │ │ └── Answer.AcompB.vcf │ │ │ │ └── Compare │ │ │ │ │ ├── README │ │ │ │ │ ├── Answer.intersect.vcf │ │ │ │ │ ├── Answer.AcompB.vcf │ │ │ │ │ └── Answer.BcompA.vcf │ │ │ ├── UnionTests │ │ │ │ ├── testUniqueSampleSetsDifferentVariantSets │ │ │ │ │ └── README │ │ │ │ ├── testOverlappingSamplesDifferentVariantSets │ │ │ │ │ └── README │ │ │ │ ├── testDifferentAltsAdded │ │ │ │ │ └── README │ │ │ │ └── testOverlappingSampleSameVariantSet │ │ │ │ │ └── README │ │ │ ├── IntersectTests │ │ │ │ ├── Match_Sample │ │ │ │ │ ├── RefOrAltDifferent │ │ │ │ │ │ ├── StatAnswer.txt │ │ │ │ │ │ ├── README │ │ │ │ │ │ └── Answer.vcf │ │ │ │ │ ├── DifferentAlts │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── StatAnswer.txt │ │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ └── input2.vcf │ │ │ │ │ ├── SameAltDifferentHet │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── StatAnswer.txt │ │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ └── input2.vcf │ │ │ │ │ ├── DifferentVarsSameSamples │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── StatAnswer.txt │ │ │ │ │ │ └── Answer.vcf │ │ │ │ │ └── MismatchingSamples │ │ │ │ │ │ ├── StatAnswer.txt │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ └── input2.vcf │ │ │ │ ├── Het_Only │ │ │ │ │ ├── UniqueSamples │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ └── input2.vcf │ │ │ │ │ ├── MultipleAlts │ │ │ │ │ │ ├── README │ │ │ │ │ │ └── Answer.vcf │ │ │ │ │ ├── HomoAlt │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ └── input2.vcf │ │ │ │ │ ├── HomoRef │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ └── input2.vcf │ │ │ │ │ └── SameSampleDifferentGeno │ │ │ │ │ │ ├── README │ │ │ │ │ │ └── Answer.vcf │ │ │ │ ├── Homo_Alt │ │ │ │ │ ├── UniqueSamples │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ └── input2.vcf │ │ │ │ │ ├── HomoRef │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ └── input2.vcf │ │ │ │ │ ├── RefOrAltDifferent │ │ │ │ │ │ ├── README │ │ │ │ │ │ └── Answer.vcf │ │ │ │ │ ├── SameSampleDifferentGeno │ │ │ │ │ │ ├── README │ │ │ │ │ │ └── Answer.vcf │ │ │ │ │ └── DifferentAlts │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ └── input2.vcf │ │ │ │ ├── Het_Or_Homo_Alt │ │ │ │ │ ├── UniqueSamples │ │ │ │ │ │ └── README │ │ │ │ │ ├── MultipleAlts │ │ │ │ │ │ ├── README │ │ │ │ │ │ └── Answer.vcf │ │ │ │ │ ├── SameSampleDifferentGeno │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ ├── input2.vcf │ │ │ │ │ │ └── Answer.vcf │ │ │ │ │ ├── HomoRef │ │ │ │ │ │ ├── README │ │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ │ ├── input1.vcf │ │ │ │ │ │ └── input2.vcf │ │ │ │ │ └── RefOrAltDifferent │ │ │ │ │ │ ├── README │ │ │ │ │ │ └── Answer.vcf │ │ │ │ ├── Alt │ │ │ │ │ ├── RefOrAltDifferent │ │ │ │ │ │ ├── README │ │ │ │ │ │ └── Answer.vcf │ │ │ │ │ └── DifferentPosAndChr │ │ │ │ │ │ ├── README │ │ │ │ │ │ └── Answer.vcf │ │ │ │ ├── Pos │ │ │ │ │ └── DifferentPosAndChr │ │ │ │ │ │ └── README │ │ │ │ └── Homo_Ref │ │ │ │ │ ├── NoHetOrNoHomoAlt │ │ │ │ │ ├── README │ │ │ │ │ └── Answer.vcf │ │ │ │ │ ├── BaseTest │ │ │ │ │ ├── README │ │ │ │ │ ├── input1.vcf │ │ │ │ │ ├── input2.vcf │ │ │ │ │ └── Answer.vcf │ │ │ │ │ └── Test2 │ │ │ │ │ ├── README │ │ │ │ │ └── Answer.vcf │ │ │ └── ComplementTests │ │ │ │ ├── Exact │ │ │ │ ├── DifferentPosOrChr │ │ │ │ │ ├── README │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ ├── input1.vcf │ │ │ │ │ └── input2.vcf │ │ │ │ ├── ExactGenotypeTest │ │ │ │ │ ├── README │ │ │ │ │ └── Answer.vcf │ │ │ │ ├── SameSampleDifferentGeno │ │ │ │ │ ├── README │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ ├── input2.vcf │ │ │ │ │ └── input1.vcf │ │ │ │ └── RefOrAltDifferent │ │ │ │ │ ├── README │ │ │ │ │ └── Answer.vcf │ │ │ │ ├── Het_or_Homo_Alt │ │ │ │ ├── DifferentPosOrChr │ │ │ │ │ ├── README │ │ │ │ │ ├── Answer.vcf │ │ │ │ │ ├── input1.vcf │ │ │ │ │ └── input2.vcf │ │ │ │ ├── HetHomoAltGenotypeTest │ │ │ │ │ ├── README │ │ │ │ │ └── Answer.vcf │ │ │ │ └── RefOrAltDifferent │ │ │ │ │ ├── README │ │ │ │ │ └── Answer.vcf │ │ │ │ └── Alt │ │ │ │ ├── SameSampleDifferentNumberVars │ │ │ │ ├── README │ │ │ │ ├── Answer.vcf │ │ │ │ ├── input2.vcf │ │ │ │ └── input1.vcf │ │ │ │ ├── UniqueSampleDifferentNumberVars │ │ │ │ ├── README │ │ │ │ ├── Answer.vcf │ │ │ │ ├── input2.vcf │ │ │ │ └── input1.vcf │ │ │ │ ├── RefOrAltDifferent │ │ │ │ ├── README │ │ │ │ ├── Answer.vcf │ │ │ │ ├── input1.vcf │ │ │ │ └── input2.vcf │ │ │ │ └── DifferentPosOrChr │ │ │ │ ├── README │ │ │ │ └── Answer.vcf │ │ └── .DS_Store │ ├── .DS_Store │ └── java │ │ └── rules │ │ └── OnFail.java ├── .DS_Store └── main │ ├── java │ └── vtc │ │ ├── datastructures │ │ ├── Pool.java │ │ ├── VariantPoolException.java │ │ ├── InvalidInputFileException.java │ │ ├── VariantPool.java │ │ ├── SupportedFileType.java │ │ └── VariantPoolLight.java │ │ ├── Engine.java │ │ ├── tools │ │ ├── varstats │ │ │ ├── AltType.java │ │ │ └── VarStatsException.java │ │ ├── setoperator │ │ │ ├── MismatchType.java │ │ │ ├── operation │ │ │ │ └── InvalidOperationException.java │ │ │ ├── Operator.java │ │ │ └── ComplementType.java │ │ └── arupfrequencycalculator │ │ │ └── NoCallRegionList.java │ │ └── VTClog4jAppender.java │ └── resources │ └── log4j.properties ├── lib ├── sam-1.96.jar ├── junit-4.11.jar ├── picard-1.96.jar ├── httpcore-4.3.jar ├── json-20140107.jar ├── log4j-1.2.17.jar ├── tribble-1.96.jar ├── variant-1.96.jar ├── argparse4j-0.4.1.jar ├── fluent-hc-4.3.1.jar ├── httpclient-4.3.1.jar ├── httpmime-4.3.1.jar ├── commons-codec-1.6.jar ├── commons-math3-3.2.jar ├── commons-logging-1.1.3.jar ├── httpclient-cache-4.3.1.jar ├── argparse4j-0.4.1-sources.jar └── argparse4j-head-19Nov2013.jar ├── images └── so_syntax.png ├── test_data ├── TSVC_variants.vcf.gz ├── UnionTests │ ├── Test4 │ │ └── README │ ├── Test1 │ │ └── README │ ├── Test3 │ │ └── README │ └── Test2 │ │ ├── README │ │ └── Answer.vcf └── IntersectTests │ ├── Match_Sample │ └── Test1 │ │ ├── README │ │ └── Answer.vcf │ ├── Het_Or_Homo_Alt │ ├── Test1 │ │ ├── input2.percent.txt │ │ ├── input1.percent.txt │ │ ├── README │ │ └── Answer.vcf │ └── Test2 │ │ ├── README │ │ └── Answer.vcf │ ├── Het_Only │ └── Test1 │ │ ├── README │ │ └── Answer.vcf │ └── Homo_Ref │ ├── Test1 │ ├── README │ └── Answer.vcf │ └── Test2 │ ├── README │ └── Answer.vcf ├── .settings ├── org.eclipse.m2e.core.prefs └── org.eclipse.jdt.core.prefs ├── .project └── .classpath /.gitignore: -------------------------------------------------------------------------------- 1 | /target 2 | /src/main/java/vtc/VTC.properties 3 | *.log 4 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/MiscSetOperTests/Compare/AcompB.out.vcf: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/MiscSetOperTests/Compare/BcompA.out.vcf: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/MiscSetOperTests/Compare/intersect.out.vcf: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/MiscSetOperTests/Compare/union.out.vcf: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/.DS_Store -------------------------------------------------------------------------------- /src/test/resources/test_data/phenos/pheno3: -------------------------------------------------------------------------------- 1 | 2 ID_1 2 | 1 ID_2 3 | 1 ID_3 4 | 2 ID_4 -------------------------------------------------------------------------------- /src/test/resources/test_data/phenos/pheno4: -------------------------------------------------------------------------------- 1 | ID_30000 2 2 | ID_30001 1 3 | ID_30002 2 -------------------------------------------------------------------------------- /lib/sam-1.96.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/sam-1.96.jar -------------------------------------------------------------------------------- /lib/junit-4.11.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/junit-4.11.jar -------------------------------------------------------------------------------- /lib/picard-1.96.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/picard-1.96.jar -------------------------------------------------------------------------------- /src/test/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/.DS_Store -------------------------------------------------------------------------------- /images/so_syntax.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/images/so_syntax.png -------------------------------------------------------------------------------- /lib/httpcore-4.3.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/httpcore-4.3.jar -------------------------------------------------------------------------------- /lib/json-20140107.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/json-20140107.jar -------------------------------------------------------------------------------- /lib/log4j-1.2.17.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/log4j-1.2.17.jar -------------------------------------------------------------------------------- /lib/tribble-1.96.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/tribble-1.96.jar -------------------------------------------------------------------------------- /lib/variant-1.96.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/variant-1.96.jar -------------------------------------------------------------------------------- /lib/argparse4j-0.4.1.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/argparse4j-0.4.1.jar -------------------------------------------------------------------------------- /lib/fluent-hc-4.3.1.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/fluent-hc-4.3.1.jar -------------------------------------------------------------------------------- /lib/httpclient-4.3.1.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/httpclient-4.3.1.jar -------------------------------------------------------------------------------- /lib/httpmime-4.3.1.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/httpmime-4.3.1.jar -------------------------------------------------------------------------------- /lib/commons-codec-1.6.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/commons-codec-1.6.jar -------------------------------------------------------------------------------- /lib/commons-math3-3.2.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/commons-math3-3.2.jar -------------------------------------------------------------------------------- /lib/commons-logging-1.1.3.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/commons-logging-1.1.3.jar -------------------------------------------------------------------------------- /src/test/resources/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/.DS_Store -------------------------------------------------------------------------------- /lib/httpclient-cache-4.3.1.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/httpclient-cache-4.3.1.jar -------------------------------------------------------------------------------- /test_data/TSVC_variants.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/test_data/TSVC_variants.vcf.gz -------------------------------------------------------------------------------- /lib/argparse4j-0.4.1-sources.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/argparse4j-0.4.1-sources.jar -------------------------------------------------------------------------------- /lib/argparse4j-head-19Nov2013.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/lib/argparse4j-head-19Nov2013.jar -------------------------------------------------------------------------------- /.settings/org.eclipse.m2e.core.prefs: -------------------------------------------------------------------------------- 1 | activeProfiles= 2 | eclipse.preferences.version=1 3 | resolveWorkspaceProjects=true 4 | version=1 5 | -------------------------------------------------------------------------------- /src/test/resources/test_data/TSVC_variants.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/TSVC_variants.vcf.gz -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/AddCHR/README: -------------------------------------------------------------------------------- 1 | This tests the header repair function. 2 | I removed both filters, the AF info and the GT format rows. -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/NoCall/README: -------------------------------------------------------------------------------- 1 | This tests the header repair function. 2 | I removed both filters, the AF info and the GT format rows. -------------------------------------------------------------------------------- /test_data/UnionTests/Test4/README: -------------------------------------------------------------------------------- 1 | This will test unioning two vcfs with two overlapping samples, one 2 | non-overlapping sample, and no overlapping variants. 3 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/RepairHeader/README: -------------------------------------------------------------------------------- 1 | This tests the header repair function. 2 | I removed both filters, the AF info and the GT format rows. -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/SamplesWithinSameFile/README: -------------------------------------------------------------------------------- 1 | This tests the functionality of using different samples 2 | within the files for set operations. -------------------------------------------------------------------------------- /test_data/UnionTests/Test1/README: -------------------------------------------------------------------------------- 1 | This will test unioning two vcfs with different samples. Any Samples not 2 | in common between the two vcfs will be added with NO_CALL genotypes. -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/union/u_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/union/u_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Alt/i_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/intersect/Alt/i_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Pos/i_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/intersect/Pos/i_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/Complement/Alt/i_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/Complement/Alt/i_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/Complement/Exact/i_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/Complement/Exact/i_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Het_Only/i_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/intersect/Het_Only/i_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Homo_Alt/i_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/intersect/Homo_Alt/i_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Homo_Ref/i_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/intersect/Homo_Ref/i_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/UnionTests/testUniqueSampleSetsDifferentVariantSets/README: -------------------------------------------------------------------------------- 1 | Two VCF with unique sets of samples. Variants unique to one VCF will have NOCALLs(./.) for the samples in the other file. -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Match_Sample/i_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/intersect/Match_Sample/i_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/UnionTests/testOverlappingSamplesDifferentVariantSets/README: -------------------------------------------------------------------------------- 1 | This will test unioning two vcfs with two overlapping samples, one 2 | non-overlapping sample, and no overlapping variants. 3 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Het_Or_Homo_Alt/i_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/intersect/Het_Or_Homo_Alt/i_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/Complement/Het_or_Homo_Alt/i_test1_out.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/Complement/Het_or_Homo_Alt/i_test1_out.vcf.idx -------------------------------------------------------------------------------- /src/main/java/vtc/datastructures/Pool.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.datastructures; 5 | 6 | 7 | /** 8 | * @author markebbert 9 | * 10 | */ 11 | public interface Pool { 12 | 13 | public String getPoolID(); 14 | } 15 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/union/testUniqueSampleSetsDifferentVariantSets.vcf.idx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mebbert/VariantToolChest/HEAD/src/test/resources/test_data/OUTPUT/union/testUniqueSampleSetsDifferentVariantSets.vcf.idx -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/RefOrAltDifferent/StatAnswer.txt: -------------------------------------------------------------------------------- 1 | CHR POS REF ALT Num_Match Percent_Match Num_Mismatch Percent_Mismatch Num_PartialMatch Percent_PartialMatch Num_Total 2 | 20 17330 T A 2 100.0 0 NA 0 NA 2 -------------------------------------------------------------------------------- /src/main/java/vtc/Engine.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc; 5 | 6 | /** 7 | * @author markebbert 8 | * 9 | */ 10 | public interface Engine { 11 | 12 | // TODO: define important methods 13 | 14 | //Kevin was here. 15 | } 16 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/DifferentAlts/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with all samples overlapping. 2 | Using the Match_Sample test all variants should pass even though 3 | different alts are present. 4 | 5 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/PrintIntermediate/README: -------------------------------------------------------------------------------- 1 | This test if the print intermediate files option is functional. 2 | The last output should be the name given for the output and generic names 3 | are given to the intermediate files. -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/SameAltDifferentHet/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with all samples overlapping. 2 | Using the Match_Sample test all variants should pass even though 3 | different alts are present. 4 | 5 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/DifferentVarsSameSamples/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with all samples overlapping. 2 | Using the Match_Sample test all variants should pass even though 3 | different alts are present. 4 | 5 | -------------------------------------------------------------------------------- /src/main/java/vtc/tools/varstats/AltType.java: -------------------------------------------------------------------------------- 1 | package vtc.tools.varstats; 2 | 3 | public enum AltType { 4 | SNV, 5 | MNP, 6 | INDEL, 7 | INSERTION, 8 | DELETION, 9 | STRUCTURAL_INDEL, 10 | STRUCTURAL_INSERTION, 11 | STRUCTURAL_DELETION; 12 | } 13 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/Compare/README: -------------------------------------------------------------------------------- 1 | This tests the --compare option. 2 | There should be 4 files output 3 | (1) AcompB.vcf 4 | (2) BcompA.vcf 5 | (3) intersect.vcf 6 | (4) union.vcf 7 | 8 | If any other files appear there is a problem. -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/MismatchingSamples/StatAnswer.txt: -------------------------------------------------------------------------------- 1 | CHR POS REF ALT Num_Match Percent_Match Num_Mismatch Percent_Mismatch Num_PartialMatch Percent_PartialMatch Num_Total 2 | 20 14370 G A 1 100.0 0 NA 0 NA 1 3 | 20 17330 T A 0 NA 1 100.0 0 NA 1 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/DifferentAlts/StatAnswer.txt: -------------------------------------------------------------------------------- 1 | CHR POS REF ALT Num_Match Percent_Match Num_Mismatch Percent_Mismatch Num_PartialMatch Percent_PartialMatch Num_Total 2 | 20 1110696 A G,T 3 100.0 0 NA 0 NA 3 3 | 20 1234567 GTC G,GTCT 3 100.0 0 NA 0 NA 3 -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/DifferentPosOrChr/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | If the position or chromosome is different then variant is included from the first file 3 | 4 | Expected result: 5 | 20 14371 Pass 6 | 21 17330 Pass 7 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/SameAltDifferentHet/StatAnswer.txt: -------------------------------------------------------------------------------- 1 | CHR POS REF ALT Num_Match Percent_Match Num_Mismatch Percent_Mismatch Num_PartialMatch Percent_PartialMatch Num_Total 2 | 20 1110696 A G,T 2 66.7 1 33.3 0 NA 3 3 | 20 1234567 GTC G,GTCT 0 NA 0 NA 3 100.0 3 -------------------------------------------------------------------------------- /.settings/org.eclipse.jdt.core.prefs: -------------------------------------------------------------------------------- 1 | eclipse.preferences.version=1 2 | org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 3 | org.eclipse.jdt.core.compiler.compliance=1.6 4 | org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning 5 | org.eclipse.jdt.core.compiler.source=1.6 6 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Het_or_Homo_Alt/DifferentPosOrChr/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | If the position or chromosome is different then variant is included from the first file 3 | 4 | Expected result: 5 | 20 14371 Pass 6 | 21 17330 Pass 7 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/UniqueSamples/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the no overlapping samples using the 2 | Het option. 3 | 4 | Expected result: All should pass because every sample has a het genotype 5 | 20 14370 Pass 6 | 20 17330 Pass 7 | 20 1230237 Pass -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/UniqueSamples/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the no overlapping samples using the 2 | Het option. 3 | 4 | Expected result: All should pass because every sample has a het genotype 5 | 20 14370 Pass 6 | 20 17330 Pass 7 | 20 1230237 Pass -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/UniqueSamples/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the no overlapping samples using the 2 | Het option. 3 | 4 | Expected result: All should pass because every sample has a het genotype 5 | 20 14370 Pass 6 | 20 17330 Pass 7 | 20 1230237 Pass -------------------------------------------------------------------------------- /src/test/resources/test_data/phenos/pheno2: -------------------------------------------------------------------------------- 1 | ID_1 2 2 | ID_2 1 3 | ID_3 1 4 | ID_4 1 5 | ID_5 1 6 | ID_6 2 7 | ID_7 2 8 | ID_8 2 9 | ID_9 2 10 | ID_10 1 11 | ID_11 -9 12 | ID_12 NA 13 | ID_13 0 14 | ID_14 . 15 | ID_15 - 16 | ID_16 x 17 | ID_17 X 18 | ID_18 N/A 19 | ID_19 -99999 20 | ID_20 -9.99 -------------------------------------------------------------------------------- /src/main/java/vtc/tools/setoperator/MismatchType.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.tools.setoperator; 5 | 6 | /** 7 | * @author markebbert 8 | * 9 | */ 10 | public enum MismatchType { 11 | 12 | Mismatch, //Is a mismatch in match samples 13 | PartialMatch //Is a partial match in match samples 14 | 15 | } 16 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/MultipleAlts/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | Het option. The Het option requires that the samples contain two different alleles. 3 | 4 | Expected result: 5 | 20 17330 Pass 6 | 20 1110696 Pass 7 | 20 1234567 Fail No common alts between all samples -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/MismatchingSamples/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the exact same samples using the 2 | MATCH_SAMPLE option. This will require that all samples match themselves 3 | across variant pools. 4 | 5 | Expected result: 6 | 20 14370 Pass 7 | 20 17330 Fail for non-matching sample genotype 8 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/ExactGenotypeTest/README: -------------------------------------------------------------------------------- 1 | This tests if the exact function is working. 2 | If all genotypes are the same they are excluded. 3 | 4 | Expected result: 5 | 20 14370 Fail same genotypes 6 | 20 17330 Fail same genotypes 7 | 20 1110696 Pass one genotype is different 8 | 20 1234567 Pass one genotype is different 9 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/MultipleAlts/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | Het option. The Het option requires that the samples contain two different alleles. 3 | 4 | Expected result: 5 | 20 17330 Pass 6 | 20 1110696 Pass 7 | 20 1234567 Fail No common alts between all samples -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/HomoRef/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | Using the Homo_Alt command only variants that are homozygous 3 | alternate will be returned. This tests for homozygous reference 4 | calls. 5 | 6 | Expected result: 7 | 20 1110696 Pass 8 | 20 1230237 Fail for Homo Ref 9 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/SameSampleDifferentNumberVars/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | input1 has 2 vars and input2 has 1 var. This tests if 3 | the complement works with the same sample in each file. 4 | 5 | Expected result: 6 | 20 1110696 Fail because it is the same in both files 7 | 20 1234567 Pass -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/UniqueSampleDifferentNumberVars/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | input1 has 2 vars and input2 has 1 var. This tests if 3 | the complement works with two different samples between the files. 4 | 5 | Expected result: 6 | 20 1110696 Fail because it is the same in both files 7 | 20 1234567 Pass -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Alt/RefOrAltDifferent/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | homo_alt. This tests if variants with REF or ALT columns that are different are excluded. 3 | 4 | Expected result: 5 | 20 17330 Pass 6 | 20 1110696 Fail for different reference allele 7 | 20 1230237 Fail for different alternate allele -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/DifferentVarsSameSamples/StatAnswer.txt: -------------------------------------------------------------------------------- 1 | CHR POS REF ALT Num_Match Percent_Match Num_Mismatch Percent_Mismatch Num_PartialMatch Percent_PartialMatch Num_Total 2 | 20 14370 G A 2 66.7 1 33.3 0 NA 3 3 | 20 17330 T A 2 66.7 0 NA 1 33.3 3 4 | 20 1110696 A G,T 0 NA 1 33.3 2 66.7 3 5 | 20 1234567 GTC G,GTCT 1 33.3 0 NA 2 66.7 3 6 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/RefOrAltDifferent/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | homo_alt. This tests if variants with REF or ALT columns that are different are excluded. 3 | 4 | Expected result: 5 | 20 17330 Fail 6 | 20 1110696 Pass for different reference allele 7 | 20 1230237 Pass for different alternate allele -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/HomoAlt/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | Het option. The Het option requires that the samples contain one ref and one alt allele. Of 3 | course homozygotes will cause exclusion. 4 | 5 | Expected result: 6 | 20 14370 Fail for homo alt 7 | 20 17330 Pass 8 | 20 1230237 Fail for homo alt -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/HomoRef/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | Het option. The Het option requires that the samples contain one ref and one alt allele. Of 3 | course homozygotes will cause exclusion. 4 | 5 | Expected result: 6 | 20 14370 Fail for homo ref 7 | 20 17330 Pass 8 | 20 1230237 Fail for homo ref -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/SameSampleDifferentGeno/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | het_homo_alt option. If the overlapping sample has a differnt genotype in one file than in 3 | the other it should not be added. 4 | 5 | Expected result: 6 | 20 14370 Pass using the second genotype 7 | 20 17330 Pass -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/RefOrAltDifferent/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | homo_alt. This tests if variants with REF or ALT columns that are different are excluded. 3 | 4 | Expected result: 5 | 20 17330 Pass 6 | 20 1110696 Fail for different reference allele 7 | 20 1230237 Fail for different alternate allele -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Het_or_Homo_Alt/HetHomoAltGenotypeTest/README: -------------------------------------------------------------------------------- 1 | This tests if the exact function is working. 2 | If all genotypes are het or homo alt same they are excluded. 3 | 4 | Expected result: 5 | 20 14370 Fail same genotypes 6 | 20 17330 Fail same genotypes 7 | 20 1110696 Pass one genotype homo alt for different alt 8 | 20 1234567 Pass one genotype homo ref 9 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Pos/DifferentPosAndChr/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | If the position or chromosome is different then variant is excluded 3 | 4 | Expected result: 5 | 20 14370 Fail for different positions 6 | 20 17330 Fail for different chromosomes 7 | 20 1110696 Pass 8 | 20 1230237 Pass 9 | 20 1234567 Pass 10 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/DifferentPosOrChr/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | If the position or chromosome is different then variant is excluded 3 | 4 | Expected result: 5 | 20 14370 Pass 6 | 20 17330 Pass 7 | 20 1110696 Fail They are the same 8 | 20 1230237 Fail They are the same 9 | 20 1234567 Fail They are the same 10 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/HomoRef/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | Het option. The Het option requires that the samples contain one ref and one alt allele. Of 3 | course homozygotes will cause exclusion. 4 | 5 | Expected result: 6 | 20 14370 Fail for homo ref 7 | 20 17330 Pass 8 | 20 1230237 Fail for homo ref -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/RefOrAltDifferent/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | het_homo_alt. This tests if variants with REF or ALT columns that are different are excluded. 3 | 4 | Expected result: 5 | 20 17330 Pass 6 | 20 1110696 Fail for different reference allele 7 | 20 1230237 Fail for different alternate allele -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Alt/DifferentPosAndChr/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | If the position or chromosome is different then variant is excluded 3 | 4 | Expected result: 5 | 20 14370 Fail for different positions 6 | 20 17330 Fail for different chromosomes 7 | 20 1110696 Pass 8 | 20 1230237 Fail it doesn't have an Alt 9 | 20 1234567 Pass 10 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/SameSampleDifferentGeno/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | Het option. If the overlapping sample has a differnt genotype in one file than in 3 | the other it should not be added. 4 | 5 | Expected result: 6 | 20 14370 Pass using the first genotype 7 | 20 17330 Pass 8 | 20 1230237 Fail for different genotype alt -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/SameSampleDifferentGeno/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | homo_alt option. If the overlapping sample has a differnt genotype in one file than in 3 | the other it should not be added. 4 | 5 | Expected result: 6 | 20 14370 Fail for different alt allele 7 | 20 14371 Fail for different genotype 8 | 20 17330 Pass -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Ref/NoHetOrNoHomoAlt/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | This will test that only vairants with a homo ref genotype are included. 3 | 4 | Expected result: 5 | 20 14370 Fail for Homo Alt and Het 6 | 20 17330 Fail for Het 7 | 20 1110696 Fail for het & homo alt 8 | 20 1230237 Pass 9 | 20 1234567 Fail for no Homo Ref 10 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/SameSampleDifferentGeno/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one sample in each file named the same. 2 | Tests whether it will elimitate the variant when genotypes are different for the same individual. 3 | 4 | Expected result: 5 | 20 14370 Fail all genotypes are the same. 6 | 20 17330 Fail because the same sample genotypes are different 7 | 20 1110696 Pass -------------------------------------------------------------------------------- /test_data/IntersectTests/Match_Sample/Test1/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the exact same samples using the 2 | MATCH_SAMPLE option. This will require that all samples match themselves 3 | across variant pools. 4 | 5 | Expected result: 6 | 20 14370 Pass 7 | 20 17330 Fail for non-matching sample genotype 8 | 20 1110696 Fail for non-matching sample genotype 9 | 20 1230237 Pass 10 | 20 1234567 Pass 11 | -------------------------------------------------------------------------------- /test_data/UnionTests/Test3/README: -------------------------------------------------------------------------------- 1 | This will test unioning two vcfs with no overlapping samples. One var 2 | has a different alt. This should add both alts to the line. If we 3 | encounter the same sample with different genotypes, it should be 4 | omitted because we don't know which one to report. 5 | 6 | Expected result: 7 | 20 14370 Pass 8 | 20 17330 Pass 9 | 20 1110696 Pass 10 | 20 1230237 Pass 11 | 20 1234567 Pass 12 | -------------------------------------------------------------------------------- /src/main/java/vtc/datastructures/VariantPoolException.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.datastructures; 5 | 6 | /** 7 | * @author markebbert 8 | * 9 | */ 10 | public class VariantPoolException extends Exception{ 11 | 12 | /** 13 | * 14 | */ 15 | private static final long serialVersionUID = 492884518173784168L; 16 | 17 | public VariantPoolException(String message){ 18 | super(message); 19 | } 20 | 21 | } 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/RefOrAltDifferent/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | homo_alt. This tests if variants with REF or ALT columns that are different are included form the first file. 3 | 4 | Expected result: 5 | 20 17330 Fail because of all genotypes are the same 6 | 20 1110696 Pass for different reference allele 7 | 20 1230237 Pass for different alternate allele -------------------------------------------------------------------------------- /src/main/java/vtc/datastructures/InvalidInputFileException.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.datastructures; 5 | 6 | /** 7 | * @author markebbert 8 | * 9 | */ 10 | public class InvalidInputFileException extends Exception { 11 | 12 | /** 13 | * 14 | */ 15 | private static final long serialVersionUID = 8737568813714627096L; 16 | 17 | public InvalidInputFileException(String message){ 18 | super(message); 19 | } 20 | } 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/DifferentAlts/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | Using the Homo_Alt command only variants that are homozygous 3 | alternate, with the same alternate allele, will be returned. 4 | This tests for homozygous alternate calls that have different alternates. 5 | 6 | Expected result: 7 | 20 1110696 Pass 8 | 20 1234567 Fail because no alt is common among all samples 9 | -------------------------------------------------------------------------------- /src/main/java/vtc/tools/varstats/VarStatsException.java: -------------------------------------------------------------------------------- 1 | package vtc.tools.varstats; 2 | 3 | public class VarStatsException extends Exception{ 4 | 5 | /** 6 | * 7 | */ 8 | private static final long serialVersionUID = 7052008735448836061L; 9 | 10 | public VarStatsException() {} 11 | 12 | //Constructor that accepts a message 13 | public VarStatsException(String message) 14 | { 15 | super(message); 16 | } 17 | } 18 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Het_or_Homo_Alt/RefOrAltDifferent/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the one overlapping sample using the 2 | het_homo_alt. This tests if variants with REF or ALT columns that are different are included form the first file. 3 | 4 | Expected result: 5 | 20 17330 Fail because of all genotypes are the same 6 | 20 1110696 Pass for different reference allele 7 | 20 1230237 Pass for different alternate allele -------------------------------------------------------------------------------- /test_data/IntersectTests/Het_Or_Homo_Alt/Test1/input2.percent.txt: -------------------------------------------------------------------------------- 1 | CHR POS REF ALT HOMO_ALT_percent HET_ALT_percent HET_percent HOMO_REF_percent 2 | chr20 14370 G 0.3333333333333333 0.0 0.3333333333333333 0.3333333333333333 3 | chr20 17330 T 0.0 0.0 0.3333333333333333 0.6666666666666666 4 | chr20 1110696 A 0.3333333333333333 0.6666666666666666 0.0 0.0 5 | chr20 1230237 T 0.0 0.0 0.0 1.0 6 | chr20 1234567 GTC 0.3333333333333333 0.0 0.6666666666666666 0.0 7 | -------------------------------------------------------------------------------- /test_data/UnionTests/Test2/README: -------------------------------------------------------------------------------- 1 | This will test unioning two vcfs with an overlapping sample. If we 2 | encounter the same sample with different genotypes, it should be 3 | omitted because we don't know which one to report. 4 | 5 | Expected result: 6 | 20 14370 Pass 7 | 20 17330 Fail for different refs 8 | 20 1110696 Fail for matching sample with different genotype 9 | 20 1230237 Pass 10 | 20 1234567 Fail for matching sample with different genotype 11 | -------------------------------------------------------------------------------- /src/test/resources/test_data/UnionTests/testDifferentAltsAdded/README: -------------------------------------------------------------------------------- 1 | This will test unioning two vcfs with no overlapping samples. One var 2 | has a different alt. This should add both alts to the line. If we 3 | encounter the same sample with different genotypes, it should be 4 | omitted because we don't know which one to report. 5 | 6 | Expected result: 7 | 20 14370 Pass 8 | 20 17330 Pass 9 | 20 1110696 Pass 10 | 20 1230237 Pass 11 | 20 1234567 Pass 12 | -------------------------------------------------------------------------------- /test_data/IntersectTests/Het_Or_Homo_Alt/Test1/input1.percent.txt: -------------------------------------------------------------------------------- 1 | CHR POS REF ALT HOMO_ALT_percent HET_ALT_percent HET_percent HOMO_REF_percent 2 | chr20 14370 G A 0.3333333333333333 0.0 0.3333333333333333 0.3333333333333333 3 | chr20 17330 T A 0.0 0.0 0.6666666666666666 0.3333333333333333 4 | chr20 1110696 A G,T 0.3333333333333333 0.6666666666666666 0.0 0.0 5 | chr20 1230237 T 0.0 0.0 0.0 1.0 6 | chr20 1234567 GTC G,GTCT 0.3333333333333333 0.0 0.6666666666666666 0.0 7 | -------------------------------------------------------------------------------- /src/main/java/vtc/tools/setoperator/operation/InvalidOperationException.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.tools.setoperator.operation; 5 | 6 | /** 7 | * @author markebbert 8 | * 9 | */ 10 | public class InvalidOperationException extends Exception{ 11 | 12 | /** 13 | * 14 | */ 15 | private static final long serialVersionUID = 492884518173784168L; 16 | 17 | public InvalidOperationException(String message){ 18 | super(message); 19 | } 20 | 21 | } 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/RefOrAltDifferent/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the two overlapping samples using the 2 | Match_Sample. This tests if variants with REF or ALT columns that are different are excluded and makes sure 3 | that match sample is checking actual genotype and not just the numbers. 4 | 5 | 6 | Expected result: 7 | 20 17330 Pass 8 | 20 1110696 Fail for different reference allele 9 | 20 1230237 Fail for different alternate allele -------------------------------------------------------------------------------- /test_data/IntersectTests/Het_Only/Test1/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with the on overlapping sample using the 2 | Het option. The Het option requires that the samples contain a Ref allele too, 3 | so if a sample is het for two different Alts, the variant will be excluded. Of 4 | course homozygotes will also cause exclusion. 5 | 6 | Expected result: 7 | 20 14370 Fail for homo ref 8 | 20 17330 Pass 9 | 20 1110696 Fail for Het with two different alts 10 | 20 1230237 Fail for homo ref 11 | 20 1234567 Pass 12 | -------------------------------------------------------------------------------- /test_data/IntersectTests/Homo_Ref/Test1/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | Any genotype that does not match between two samples with the same name 3 | will not be considered an intersect. This will also test that no variants with 4 | a Homo Ref sample are returned. 5 | 6 | Expected result: 7 | 20 14370 Fail for Homo Ref 8 | 20 17330 Fail for non-matching sample genotype 9 | 20 1110696 Pass 10 | 20 1230237 Fail for Homo Ref 11 | 20 1234567 Fail because no alt is common among all samples 12 | -------------------------------------------------------------------------------- /test_data/IntersectTests/Het_Or_Homo_Alt/Test1/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | Any genotype that does not match between two samples with the same name 3 | will not be considered an intersect. This will also test that no variants with 4 | a Homo Ref sample are returned. 5 | 6 | Expected result: 7 | 20 14370 Fail for Homo Ref 8 | 20 17330 Fail for non-matching sample genotype 9 | 20 1110696 Pass 10 | 20 1230237 Fail for Homo Ref 11 | 20 1234567 Fail because no alt is common among all samples 12 | -------------------------------------------------------------------------------- /src/test/resources/test_data/UnionTests/testOverlappingSampleSameVariantSet/README: -------------------------------------------------------------------------------- 1 | This will test unioning two vcfs with an overlapping sample. If we 2 | encounter the same sample with different genotypes, it should be 3 | omitted because we don't know which one to report. 4 | 5 | Expected result: 6 | 20 14370 Pass 7 | 20 17330 Fail for different refs( I think that this should actually pass - Mark W.) 8 | 20 1110696 Fail for matching sample with different genotype 9 | 20 1230237 Pass 10 | 20 1234567 Fail for matching sample with different genotype -------------------------------------------------------------------------------- /src/main/java/vtc/VTClog4jAppender.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc; 5 | 6 | import java.util.Random; 7 | 8 | import org.apache.log4j.DailyRollingFileAppender; 9 | 10 | /** 11 | * @author markebbert 12 | * 13 | */ 14 | public class VTClog4jAppender extends DailyRollingFileAppender { 15 | 16 | @Override 17 | public void setFile(String fileName) { 18 | if (fileName.indexOf("%rnd") >= 0) { 19 | Random r = new Random(); 20 | fileName = fileName.replaceAll("%rnd", Integer.toString(r.nextInt())); 21 | } 22 | super.setFile(fileName); 23 | } 24 | 25 | } 26 | -------------------------------------------------------------------------------- /src/main/java/vtc/datastructures/VariantPool.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.datastructures; 5 | 6 | import htsjdk.variant.variantcontext.VariantContext; 7 | import htsjdk.variant.vcf.VCFHeader; 8 | 9 | import java.io.File; 10 | import java.io.IOException; 11 | import java.util.TreeSet; 12 | 13 | /** 14 | * @author markebbert 15 | * 16 | */ 17 | public interface VariantPool extends Pool{ 18 | 19 | public VariantContext getNextVar() throws IOException; 20 | public TreeSet getSamples(); 21 | public VCFHeader getHeader(); 22 | public String getPoolID(); 23 | public File getFile(); 24 | 25 | } 26 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Ref/BaseTest/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with no overlapping sample. 2 | Any genotype that does not match between two samples with the same name 3 | will not be considered an intersect. This will also test that the Alt 4 | alleles intersect. Alt alleles intersect if at least one alternate allele 5 | is the same. Ref alleles must also be identical 6 | 7 | Expected result: 8 | 20 14370 Fail for different Alt alleles 9 | 20 17330 Fail for Het Alleles 10 | 20 1110696 Fail for Alt alleles 11 | 20 1230237 Pass for Homo Ref 12 | 20 1234567 Fail because no alt is common among all samples 13 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Ref/Test2/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with no overlapping sample. 2 | Any genotype that does not match between two samples with the same name 3 | will not be considered an intersect. This will also test that the Alt 4 | alleles intersect. Alt alleles intersect if at least one alternate allele 5 | is the same. Ref alleles must also be identical 6 | 7 | Expected result: 8 | 20 14370 Fail for different Alt alleles 9 | 20 17330 Fail for Het Alleles 10 | 20 1110696 Fail for Alt alleles 11 | 20 1230237 Pass for Homo Ref 12 | 20 1234567 Fail because no alt is common among all samples 13 | -------------------------------------------------------------------------------- /test_data/IntersectTests/Homo_Ref/Test2/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | Any genotype that does not match between two samples with the same name 3 | will not be considered an intersect. This will also test that the Alt 4 | alleles intersect. Alt alleles intersect if at least one alternate allele 5 | is the same. Ref alleles must also be identical 6 | 7 | Expected result: 8 | 20 14370 Fail for different Alt alleles 9 | 20 17330 Fail for different Ref alleles 10 | 20 1110696 Pass because at least one alt allele overlaps 11 | 20 1230237 Fail for Homo Ref 12 | 20 1234567 Fail because no alt is common among all samples 13 | -------------------------------------------------------------------------------- /test_data/IntersectTests/Het_Or_Homo_Alt/Test2/README: -------------------------------------------------------------------------------- 1 | This will test comparing two vcfs with one overlapping sample. 2 | Any genotype that does not match between two samples with the same name 3 | will not be considered an intersect. This will also test that the Alt 4 | alleles intersect. Alt alleles intersect if at least one alternate allele 5 | is the same. Ref alleles must also be identical 6 | 7 | Expected result: 8 | 20 14370 Fail for different Alt alleles 9 | 20 17330 Fail for different Ref alleles 10 | 20 1110696 Pass because at least one alt allele overlaps 11 | 20 1230237 Fail for Homo Ref 12 | 20 1234567 Fail because no alt is common among all samples 13 | -------------------------------------------------------------------------------- /.project: -------------------------------------------------------------------------------- 1 | 2 | 3 | VariantToolChest 4 | 5 | 6 | 7 | 8 | 9 | org.eclipse.jdt.core.javabuilder 10 | 11 | 12 | 13 | 14 | org.eclipse.m2e.core.maven2Builder 15 | 16 | 17 | 18 | 19 | 20 | org.eclipse.jdt.core.javanature 21 | org.eclipse.m2e.core.maven2Nature 22 | 23 | 24 | -------------------------------------------------------------------------------- /src/main/resources/log4j.properties: -------------------------------------------------------------------------------- 1 | # Root logger option 2 | log4j.rootLogger=INFO, file, stdout 3 | 4 | # Direct log messages to a log file 5 | log4j.appender.file=vtc.VTClog4jAppender 6 | log4j.appender.file.File=vtc.%rnd.log 7 | #log4j.appender.file.MaxFileSize=1MB 8 | #log4j.appender.file.MaxBackupIndex=1 9 | log4j.appender.file.layout=org.apache.log4j.PatternLayout 10 | log4j.appender.file.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n 11 | 12 | # Direct log messages to stdout 13 | log4j.appender.stdout=org.apache.log4j.ConsoleAppender 14 | log4j.appender.stdout.Target=System.out 15 | log4j.appender.stdout.layout=org.apache.log4j.PatternLayout 16 | log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n -------------------------------------------------------------------------------- /src/main/java/vtc/tools/setoperator/Operator.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.tools.setoperator; 5 | 6 | /** 7 | * @author markebbert 8 | * 9 | */ 10 | public enum Operator { 11 | 12 | INTERSECT("iI", "Performs intersection"), 13 | COMPLEMENT("cC", "Performs complement (i.e. substraction)"), 14 | UNION("uU", "Performs union"); 15 | 16 | private String allowedSymbols; 17 | private String description; 18 | private Operator(String allowedSymbols, String description){ 19 | this.allowedSymbols = allowedSymbols; 20 | this.description = description; 21 | } 22 | 23 | public String getDescription(){ 24 | return this.description; 25 | } 26 | 27 | public static Operator getOperator(String operString){ 28 | 29 | if(Operator.INTERSECT.allowedSymbols.contains(operString)){ 30 | return Operator.INTERSECT; 31 | } 32 | else if(Operator.COMPLEMENT.allowedSymbols.contains(operString)){ 33 | return Operator.COMPLEMENT; 34 | } 35 | else if(Operator.UNION.allowedSymbols.contains(operString)){ 36 | return Operator.UNION; 37 | } 38 | return null; 39 | } 40 | } 41 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/NoCall/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##FORMAT= 13 | ##FORMAT= 14 | ##FORMAT= 15 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 16 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 17 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP ./.:35:4 18 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/NoCall/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##FORMAT= 13 | ##FORMAT= 14 | ##FORMAT= 15 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 16 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 17 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 18 | -------------------------------------------------------------------------------- /src/main/java/vtc/tools/arupfrequencycalculator/NoCallRegionList.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.tools.arupfrequencycalculator; 5 | 6 | import java.util.ArrayList; 7 | import java.util.Iterator; 8 | 9 | /** 10 | * @author markebbert 11 | * 12 | */ 13 | public class NoCallRegionList implements Iterator { 14 | 15 | private ArrayList noCallRegions; 16 | private int currIndex; 17 | 18 | public NoCallRegionList(ArrayList noCallRegions){ 19 | this.noCallRegions = noCallRegions; 20 | currIndex = 0; 21 | } 22 | 23 | @Override 24 | public boolean hasNext() { 25 | if(currIndex < noCallRegions.size() - 1){ 26 | return true; 27 | } 28 | return false; 29 | } 30 | 31 | @Override 32 | public NoCall next() { 33 | return noCallRegions.get(currIndex++); 34 | } 35 | 36 | /** 37 | * Get the current NoCallRegion. If we've moved 38 | * past the end, return null; 39 | * @return 40 | */ 41 | public NoCall current() { 42 | try{ 43 | return noCallRegions.get(currIndex); 44 | } catch (IndexOutOfBoundsException e){ 45 | return null; 46 | } 47 | } 48 | 49 | @Override 50 | public void remove() { 51 | noCallRegions.remove(currIndex); 52 | } 53 | 54 | } 55 | -------------------------------------------------------------------------------- /src/main/java/vtc/datastructures/SupportedFileType.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.datastructures; 5 | 6 | import java.util.ArrayList; 7 | import java.util.Arrays; 8 | 9 | /** 10 | * @author markebbert 11 | * 12 | */ 13 | public enum SupportedFileType { 14 | 15 | VCF("VCF", "v", ".out.vcf", 16 | new ArrayList(Arrays.asList(".vcf,.vcf.gz".split(",")))); 17 | 18 | private String poolIDPrefix, name; 19 | private ArrayList expectedExtensions; 20 | private String defaultExtension; 21 | private SupportedFileType(String name, String poolIDPrefix, String defaultExtension, 22 | ArrayList expectedExtensions){ 23 | this.name = name; 24 | this.poolIDPrefix = poolIDPrefix; 25 | this.defaultExtension = defaultExtension; 26 | this.expectedExtensions = expectedExtensions; 27 | } 28 | 29 | public String getName(){ 30 | return this.name; 31 | } 32 | 33 | public String getPoolIDPrefix(){ 34 | return this.poolIDPrefix; 35 | } 36 | 37 | public String getDefaultExtension(){ 38 | return this.defaultExtension; 39 | } 40 | 41 | public ArrayList getExpectedExtensions(){ 42 | return this.expectedExtensions; 43 | } 44 | 45 | @Override 46 | public String toString(){ 47 | return getName(); 48 | } 49 | } 50 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Match_Sample/i_test1_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/Complement/Alt/i_test1_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Alt/i_test1_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Pos/i_test1_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/Complement/Exact/i_test1_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Homo_Alt/i_test1_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Homo_Ref/i_test1_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Het_Or_Homo_Alt/i_test1_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/Complement/Het_or_Homo_Alt/i_test1_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | -------------------------------------------------------------------------------- /src/main/java/vtc/datastructures/VariantPoolLight.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.datastructures; 5 | 6 | import java.io.File; 7 | import java.io.IOException; 8 | 9 | /** 10 | * @author markebbert 11 | * 12 | */ 13 | public class VariantPoolLight extends AbstractVariantPool { 14 | 15 | /** 16 | * @param addChr 17 | * @param poolID 18 | */ 19 | public VariantPoolLight(boolean addChr, String poolID) { 20 | super(addChr, poolID); 21 | // TODO Auto-generated constructor stub 22 | } 23 | 24 | /** 25 | * @param file 26 | * @param poolID 27 | * @param requireIndex 28 | * @param addChr 29 | * @throws IOException 30 | */ 31 | public VariantPoolLight(File file, String poolID, boolean requireIndex, 32 | boolean addChr) throws IOException { 33 | super(file, poolID, requireIndex, addChr); 34 | // TODO Auto-generated constructor stub 35 | } 36 | 37 | /** 38 | * @param inputString 39 | * @param requireIndex 40 | * @param addChr 41 | * @throws InvalidInputFileException 42 | * @throws IOException 43 | */ 44 | public VariantPoolLight(String inputString, boolean requireIndex, 45 | boolean addChr) throws InvalidInputFileException, IOException { 46 | super(inputString, requireIndex, addChr); 47 | // TODO Auto-generated constructor stub 48 | } 49 | 50 | } 51 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/PrintIntermediate/Answer.intersect.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/NoCall/Answer.AcompB.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 20 | chr20 1234567 . GTC G,GTCT . . . GT:GQ:DP ./.:35:4 -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/SameSampleDifferentNumberVars/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003 20 | 20 1234567 . GTC G,GTCT . . . GT:DP:GQ 1/1:3:40 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/UniqueSampleDifferentNumberVars/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003 20 | 20 1234567 . GTC G,GTCT . . . GT:DP:GQ 1/1:3:40 21 | -------------------------------------------------------------------------------- /src/main/java/vtc/tools/setoperator/ComplementType.java: -------------------------------------------------------------------------------- 1 | /** 2 | * 3 | */ 4 | package vtc.tools.setoperator; 5 | 6 | /** 7 | * @author markebbert 8 | * 9 | */ 10 | public enum ComplementType { 11 | 12 | HET_OR_HOMO_ALT("HET_OR_HOMO_ALT", "het_homo_alt", "All samples must be het or homo-alt for subtraction", ""), 13 | EXACT("EXACT", "exact", "Require genotypes to be identical across samples for subtraction", ""), 14 | ALT("ALT", "alt", "Ignore samples when subtracting. Only consider chr, pos, ref, alt", ""); 15 | 16 | private String name, command, briefDescription, fullDescription; 17 | private ComplementType(String name, String command, String briefDescription, String fullDescription){ 18 | this.name = name; 19 | this.command = command; 20 | this.briefDescription = briefDescription; 21 | this.fullDescription = fullDescription; 22 | } 23 | 24 | public String getName(){ 25 | return this.name; 26 | } 27 | 28 | public String getCommand(){ 29 | return this.command; 30 | } 31 | 32 | public String getBriefDescription(){ 33 | return this.briefDescription; 34 | } 35 | 36 | public String getFullDescription(){ 37 | return this.fullDescription; 38 | } 39 | 40 | @Override 41 | public String toString(){ 42 | return "'" + getCommand() + "' -- " + 43 | getBriefDescription() + "."; 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Ref/BaseTest/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 20 | 20 1230237 . T A 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Ref/BaseTest/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00002 20 | 20 1230237 . T A 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 21 | -------------------------------------------------------------------------------- /.classpath: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Ref/BaseTest/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 20 | 20 1230237 . T A . . . GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:54:7:56,60 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/NoCall/Answer.intersect.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00004 20 | 20 1110696 . A G,T . . . GT:GQ:DP:HQ 1|2:21:6:23,27 1|2:21:6:23,27 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/intersect/Het_Only/i_test1_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT ./. ./. 0/1 0/1 0/1 21 | -------------------------------------------------------------------------------- /src/test/java/rules/OnFail.java: -------------------------------------------------------------------------------- 1 | package rules; 2 | 3 | import java.io.BufferedReader; 4 | import java.io.FileNotFoundException; 5 | import java.io.FileReader; 6 | import java.io.IOException; 7 | 8 | import org.junit.rules.TestWatcher; 9 | import org.junit.runner.Description; 10 | 11 | public class OnFail extends TestWatcher { 12 | 13 | public static final String ANSI_CYAN = "\u001B[36m"; 14 | public static final String ANSI_RESET = "\u001B[0m"; 15 | public static final String ANSI_RED = "\u001B[31m"; 16 | 17 | 18 | @Override 19 | protected void failed(Throwable e, Description description) { 20 | BufferedReader br; 21 | try { 22 | 23 | br = new BufferedReader(new FileReader("src/test/java/rules/.failure.txt")); 24 | String line = null; 25 | while ((line = br.readLine()) != null) { 26 | System.out.println(ANSI_CYAN+line); 27 | } 28 | System.out.println(ANSI_RESET+""); 29 | Thread.sleep(2000); 30 | 31 | 32 | } catch (FileNotFoundException e1) { 33 | e1.printStackTrace(); 34 | } catch (IOException e1) { 35 | // TODO Auto-generated catch block 36 | e1.printStackTrace(); 37 | } catch (InterruptedException e1) { 38 | // TODO Auto-generated catch block 39 | e1.printStackTrace(); 40 | } 41 | 42 | } 43 | } -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/SameSampleDifferentNumberVars/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 2/2:35:4 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/SameSampleDifferentGeno/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003 20 | 20 17330 . T A . . . GT:GQ:DP:HQ 1/0:41:3 21 | 20 1110696 . A G,T . . . GT:DP:GQ:HQ 2/2:4:35 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/UniqueSampleDifferentNumberVars/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00002 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 2/2:35:4 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/MismatchingSamples/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 20 | 20 14370 . G A . . . GT:DP:GQ:HQ 0|0:1:48:51,51 21 | 20 17330 . T A . . . GT:GQ:DP:HQ 1|0:49:3:58,50 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/RefOrAltDifferent/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|1:3:49:58,50 1|1:5:3:65,3 1/1:3:41 1|1:5:3:65,3 -------------------------------------------------------------------------------- /test_data/IntersectTests/Het_Or_Homo_Alt/Test1/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1110696 . A G,T . . . GT:DP:GQ:HQ 1|2:6:21:23,27 2|1:0:2:18,2 2/2:4:35 1|2:6:21:23,27 2|1:0:2:18,2 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/HomoAlt/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|0:3:49:58,50 0|1:5:3:65,3 1/0:3:41 1|0:3:49:58,50 0|1:5:3:65,3 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/HomoRef/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|0:3:49:58,50 0|1:5:3:65,3 1/0:3:41 1|0:3:49:58,50 0|1:5:3:65,3 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Alt/RefOrAltDifferent/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|1:3:49:58,50 1|1:5:3:65,3 1/1:3:41 1|1:3:49:58,50 1|1:5:3:65,3 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/HomoRef/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|0:3:49:58,50 0|1:5:3:65,3 1/0:3:41 1|0:3:49:58,50 0|1:5:3:65,3 -------------------------------------------------------------------------------- /test_data/IntersectTests/Homo_Ref/Test1/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 0|0:54:7:56,60 0|0:48:4:51,51 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/HomoRef/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1110696 . A G,T . . . GT:DP:GQ:HQ 1|1:6:21:23,27 1|1:0:2:18,2 1/1:4:35 1|1:6:21:23,27 1|1:0:2:18,2 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/RefOrAltDifferent/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|1:3:49:58,50 1|1:5:3:65,3 1/1:3:41 1|1:3:49:58,50 1|1:5:3:65,3 -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/Compare/Answer.intersect.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1110696 . A G,T . . . GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 1|2:21:6:23,27 2|1:2:0:18,2 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/MiscSetOperTests/AddCHR/O_AcompB.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1110696 . A G,T . . . GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 1|2:21:6:23,27 2|1:2:0:18,2 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/MiscSetOperTests/NoCall/O_AcompB.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1110696 . A G,T . . . GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 1|2:21:6:23,27 2|1:2:0:18,2 21 | -------------------------------------------------------------------------------- /test_data/IntersectTests/Het_Or_Homo_Alt/Test2/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 NA00006 20 | 20 1110696 . A G,T . . . GT:DP:GQ:HQ 1|2:6:21:23,27 2|1:0:2:18,2 2/2:4:35 2|0:6:21:23,27 0|2:0:2:18,2 2/2:4:35 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/RefOrAltDifferent/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|0:3:49:58,50 0|1:5:3:65,3 1/0:3:41 1|0:3:49:58,50 0|1:5:3:65,3 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/DifferentAlts/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1110696 . A G,T . . . GT:DP:GQ:HQ 1|1:6:21:23,27 1|1:0:2:18,2 1/1:4:35 1|1:6:21:23,27 1|1:0:2:18,2 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/SameSampleDifferentGeno/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|1:3:49:58,50 1|1:5:3:65,3 1/1:3:41 1|1:3:49:58,50 1|1:5:3:65,3 -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/MiscSetOperTests/RepairHeader/O_AcompB.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1110696 . A G,T . . . GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 1|2:21:6:23,27 2|1:2:0:18,2 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/MiscSetOperTests/PrintIntermediate/inter.out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1110696 . A G,T . . . GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 1|2:21:6:23,27 2|1:2:0:18,2 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/MiscSetOperTests/SamplesWithinSameFile/O_AcompB.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1110696 . A G,T . . . GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 1|2:21:6:23,27 2|1:2:0:18,2 21 | -------------------------------------------------------------------------------- /test_data/IntersectTests/Homo_Ref/Test2/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 NA00006 20 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 0|0:54:7:56,60 0|0:48:4:51,51 /0:61:2 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/SameSampleDifferentGeno/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 1/1:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0/0:41:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Ref/NoHetOrNoHomoAlt/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 0|0:54:7:56,60 0|0:48:4:51,51 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/DifferentPosOrChr/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14371 . G A . . . GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 21 | 20 17330 . T A . . . GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/RefOrAltDifferent/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 . A T . . . GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 21 | 20 1230237 . T C . . . GT:GQ:DP:HQ 1|1:54:7:56,60 1|1:48:4:51,51 1/1:61:2 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Ref/Test2/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 NA00006 20 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 0|0:54:7:56,60 0|0:48:4:51,51 /0:61:2 21 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/DifferentAlts/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 . A G,T . . . GT:DP:GQ:HQ 1|1:6:21:23,27 1|1:0:2:18,2 1/1:4:35 21 | 20 1234567 . GTC G,GTCT . . . GT:GQ:DP 1/1:35:4 2/2:17:2 1/1:40:3 -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/DifferentPosOrChr/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14371 . G A . . . GT:GQ:DP:HQ 0|0:48:1:51,51 0|0:48:8:51,51 0/0:43:5:.,. 21 | 20 17330 . T A . . . GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/ExactGenotypeTest/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 . A G,T . . . GT:DP:GQ:HQ 2|2:6:21:23,27 2|1:0:2:18,2 2/2:4:35 21 | 20 1234567 . GTC G,GTCT . . . GT:DP:GQ 2/2:4:35 2/2:2:17 2/2:3:40 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/RefOrAltDifferent/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 . A T . . . GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 21 | 20 1230237 . T C . . . GT:GQ:DP:HQ 1|1:54:7:56,60 1|1:48:4:51,51 1/1:61:2 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/MismatchingSamples/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/MismatchingSamples/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/SameAltDifferentHet/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 . A G,T . . . GT:DP:GQ:HQ 2|2:6:21:23,27 0|1:0:2:18,2 1/1:4:35 21 | 20 1234567 . GTC G,GTCT . . . GT:GQ:DP 1/0:35:4 1/2:17:2 0/1:40:3 -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/AddCHR/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##FORMAT= 13 | ##FORMAT= 14 | ##FORMAT= 15 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 16 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 17 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 18 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 19 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 0/1:40:3 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/AddCHR/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##FORMAT= 13 | ##FORMAT= 14 | ##FORMAT= 15 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 16 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 17 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 18 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 19 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/RepairHeader/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##FORMAT= 13 | ##FORMAT= 14 | ##FORMAT= 15 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 16 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 17 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 18 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 19 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 0/1:40:3 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/RepairHeader/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##FORMAT= 13 | ##FORMAT= 14 | ##FORMAT= 15 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 16 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 17 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 18 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 19 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Het_or_Homo_Alt/DifferentPosOrChr/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14371 . G A . . . GT:GQ:DP:HQ 0|0:48:1:51,51 0|0:48:8:51,51 0/0:43:5:.,. 21 | 20 17330 . T A . . . GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Het_or_Homo_Alt/RefOrAltDifferent/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 . A T . . . GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 21 | 20 1230237 . T C . . . GT:GQ:DP:HQ 1|1:54:7:56,60 1|1:48:4:51,51 1/1:61:2 -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/SameSampleDifferentNumberVars/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 2/2:35:4 21 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 1/1:40:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/UniqueSampleDifferentNumberVars/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 2/2:35:4 21 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 1/1:40:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Het_or_Homo_Alt/HetHomoAltGenotypeTest/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 . A G,T . . . GT:DP:GQ:HQ 0|2:6:21:23,27 2|1:0:2:18,2 2/2:4:35 21 | 20 1234567 . GTC G,GTCT . . . GT:DP:GQ 0/0:4:35 2/2:2:17 2/2:3:40 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/SamplesWithinSameFile/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##FORMAT= 13 | ##FORMAT= 14 | ##FORMAT= 15 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 16 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 17 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 18 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 19 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 0/1:40:3 20 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/SamplesWithinSameFile/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##FORMAT= 13 | ##FORMAT= 14 | ##FORMAT= 15 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 16 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 17 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 18 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 19 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 20 | -------------------------------------------------------------------------------- /test_data/IntersectTests/Het_Only/Test1/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|0:3:49:58,50 0|1:5:3:65,3 1/0:3:41 1|0:3:49:58,50 0|1:5:3:65,3 21 | 20 1234567 . GTC G,GTCT . . . GT:DP:GQ 0/1:4:35 0/2:2:17 1/0:3:40 0/1:4:35 0/2:2:17 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/SamplesWithinSameFile/Answer.AcompB.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 20 | 20 14370 . G A . . . GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 21 | 20 17330 . T A . . . GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 22 | 20 1234567 . GTC G,GTCT . . . GT:GQ:DP 0/1:35:4 0/2:17:2 -------------------------------------------------------------------------------- /test_data/UnionTests/Test2/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00005 NA00006 20 | 20 14370 . G A . . . GT:DP:GQ:HQ 1|0:1:48:51,51 1|0:8:48:51,51 1|1:1:48:51,51 1|0:8:48:51,51 1/1:5:43 21 | 20 1230237 . T . . . . GT:DP:GQ:HQ 0|0:7:54:56,60 0|0:4:48:51,51 0|0:7:54:56,60 0|0:4:48:51,51 0/0:2:61 22 | -------------------------------------------------------------------------------- /test_data/IntersectTests/Match_Sample/Test1/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 . G A . . . GT:DP:GQ:HQ 0|0:1:48:51,51 1|0:8:48:51,51 1/1:5:43 21 | 20 1230237 . T . . . . GT:DP:GQ:HQ 0|0:7:54:56,60 0|0:4:48:51,51 0/0:2:61 22 | 20 1234567 . GTC G,GTCT . . . GT:DP:GQ 0/1:4:35 0/2:2:17 1/1:3:40 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/DifferentPosOrChr/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14371 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 0|0:48:8:51,51 0/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/DifferentPosOrChr/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 0|0:48:8:51,51 0/0:43:5:.,. 21 | 21 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/HomoRef/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 21 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/HomoRef/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 21 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/Compare/Answer.AcompB.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 . G A . . . GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 21 | 20 17330 . T A . . . GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 22 | 20 1234567 . GTC G,GTCT . . . GT:GQ:DP 0/1:35:4 0/2:17:2 0/1:40:3 -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/Compare/Answer.BcompA.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003 NA00004 NA00005 20 | 20 14370 . G A . . . GT:GQ:DP:HQ 1/1:43:5:.,. 0|0:48:1:51,51 1|0:48:8:51,51 21 | 20 17330 . T A . . . GT:GQ:DP:HQ 0/0:41:3 0|0:49:3:58,50 0|1:3:5:65,3 22 | 20 1234567 . GTC G,GTCT . . . GT:GQ:DP 1/1:40:3 0/1:35:4 0/2:17:2 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/MultipleAlts/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|0:3:49:58,50 0|1:5:3:65,3 1/0:3:41 1|0:3:49:58,50 0|1:5:3:65,3 21 | 20 1110696 . A G,T . . . GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/0:35:4 1|2:21:6:23,27 2|1:2:0:18,2 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/DifferentAlts/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 21 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 1/1:35:4 2/2:17:2 1/1:40:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/DifferentAlts/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 21 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 1/1:35:4 2/2:17:2 1/1:40:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/RepairHeader/Answer.AcompB.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 . G A . . . GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 21 | 20 17330 . T A . . . GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 22 | 20 1234567 . GTC G,GTCT . . . GT:GQ:DP 0/1:35:4 0/2:17:2 0/1:40:3 -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Het_or_Homo_Alt/DifferentPosOrChr/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14371 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 0|0:48:8:51,51 0/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Het_or_Homo_Alt/DifferentPosOrChr/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 0|0:48:8:51,51 0/0:43:5:.,. 21 | 21 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/MultipleAlts/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|0:3:49:58,50 0|1:5:3:65,3 1/0:3:41 1|0:3:49:58,50 0|1:5:3:65,3 21 | 20 1110696 . A G,T . . . GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/0:35:4 1|2:21:6:23,27 2|1:2:0:18,2 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/DifferentAlts/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 21 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 1/1:35:4 2/2:17:2 1/1:40:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/DifferentAlts/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 21 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 1/1:35:4 2/2:17:2 1/1:40:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/AddCHR/Answer.AcompB.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | chr20 14370 . G A . . . GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 21 | chr20 17330 . T A . . . GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 22 | chr20 1234567 . GTC G,GTCT . . . GT:GQ:DP 0/1:35:4 0/2:17:2 0/1:40:3 -------------------------------------------------------------------------------- /src/test/resources/test_data/MiscSetOperTests/PrintIntermediate/Answer.AcompB.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 . G A . . . GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 21 | 20 17330 . T A . . . GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 22 | 20 1234567 . GTC G,GTCT . . . GT:GQ:DP 0/1:35:4 0/2:17:2 0/1:40:3 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/SameSampleDifferentGeno/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 1|1:48:1:51,51 1|0:48:8:51,51 0/1:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 0|1:3:5:65,3 1/0:41:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/SameSampleDifferentGeno/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 1|1:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 0|1:3:5:65,3 1/0:41:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/SameAltDifferentHet/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|1:21:6:23,27 1|0:2:0:18,2 1/1:35:4 21 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 1/1:35:4 2/2:17:2 1/1:40:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/SameAltDifferentHet/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 2|2:21:6:23,27 0|1:2:0:18,2 1/1:35:4 21 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 1/0:35:4 1/2:17:2 0/1:40:3 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Exact/SameSampleDifferentGeno/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 1/1:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1/0:41:3 22 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 2/2:35:4 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/SameSampleDifferentGeno/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 14370 . G A . . . GT:GQ:DP:HQ 1|0:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 1|0:48:1:51,51 1|0:48:8:51,51 21 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|0:3:49:58,50 0|1:5:3:65,3 1/0:3:41 1|0:3:49:58,50 0|1:5:3:65,3 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/SameSampleDifferentGeno/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 14370 . G A . . . GT:GQ:DP:HQ 1|1:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 1|1:48:1:51,51 1|0:48:8:51,51 21 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|0:3:49:58,50 0|1:5:3:65,3 1/0:3:41 1|0:3:49:58,50 0|1:5:3:65,3 -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Alt/DifferentPosAndChr/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 20 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 1|2:21:6:23,27 2|1:2:0:18,2 21 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 0/1:35:4 0/2:17:2 22 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/HomoAlt/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 1|1:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 0|1:3:5:65,3 1/0:41:3 22 | 20 1230237 . T G 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|1:54:7:56,60 1|0:48:4:51,51 1/1:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/HomoAlt/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 1|1:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 0|1:3:5:65,3 1/0:41:3 22 | 20 1230237 . T G 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 1|0:54:7:56,60 1|0:48:4:51,51 1/1:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/HomoRef/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 0|1:3:5:65,3 1/0:41:3 22 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/HomoRef/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 0|1:3:5:65,3 1/0:41:3 22 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/UniqueSamples/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|1:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 0|1:3:5:65,3 1/0:41:3 22 | 20 1230237 . T G 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|1:54:7:56,60 1|0:48:4:51,51 1/0:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Only/UniqueSamples/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00006 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 1|0:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 0|1:3:5:65,3 1/0:41:3 22 | 20 1230237 . T G 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 1|0:54:7:56,60 1|0:48:4:51,51 1/0:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/HomoRef/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 0|1:3:5:65,3 1/0:41:3 22 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Het_Or_Homo_Alt/HomoRef/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/0:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|0:49:3:58,50 0|1:3:5:65,3 1/0:41:3 22 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/UniqueSamples/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 1|1:48:1:51,51 1|1:48:8:51,51 1/1:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|1:49:3:58,50 1|1:3:5:65,3 1/1:41:3 22 | 20 1230237 . T G 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 1|1:54:7:56,60 1|1:48:4:51,51 1/1:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Homo_Alt/UniqueSamples/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00006 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 1|1:48:1:51,51 1|1:48:8:51,51 1/1:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|1:49:3:58,50 1|1:3:5:65,3 1/1:41:3 22 | 20 1230237 . T G 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 1|1:54:7:56,60 1|1:48:4:51,51 1/1:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/IntersectTests/Match_Sample/DifferentVarsSameSamples/Answer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 . G A . . . GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5 21 | 20 17330 . T A . . . GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 22 | 20 1110696 . A G,T . . . GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 23 | 20 1234567 . GTC G,GTCT . . . GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 -------------------------------------------------------------------------------- /src/test/resources/test_data/OUTPUT/union/u_test2_out.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FILTER= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##contig= 15 | ##fileDate=20090805 16 | ##phasing=partial 17 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 18 | ##source=myImputationProgramV3.1 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00005 NA00006 20 | 20 14370 . G A . . . GT:DP:GQ:HQ 1|0:1:48:51,51 1|0:8:48:51,51 1|1:1:48:51,51 1|0:8:48:51,51 1/1:5:43 21 | 20 17330 . T A . . . GT:DP:GQ:HQ 1|0:3:49:58,50 0|1:5:3:65,3 0|1:3:49:58,50 0|1:5:3:65,3 1/0:3:41 22 | 20 1230237 . T . . . . GT:DP:GQ:HQ 0|0:7:54:56,60 0|0:4:48:51,51 0|0:7:54:56,60 0|0:4:48:51,51 0/0:2:61 -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/RefOrAltDifferent/input1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|1:49:3:58,50 1|1:3:5:65,3 1/1:41:3 21 | 20 1110696 rs6040355 A T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 22 | 20 1230237 . T C 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 1|1:54:7:56,60 1|1:48:4:51,51 1/1:61:2 23 | -------------------------------------------------------------------------------- /src/test/resources/test_data/ComplementTests/Alt/RefOrAltDifferent/input2.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00004 NA00005 NA00003 20 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 1|1:49:3:58,50 1|1:3:5:65,3 1/1:41:3 21 | 20 1110696 rs6040355 G T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|1:21:6:23,27 1|1:2:0:18,2 1/1:35:4 22 | 20 1230237 . T G 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 1|1:54:7:56,60 1|1:48:4:51,51 1/1:61:2 23 | --------------------------------------------------------------------------------