zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

A working version of a GATKReportDiffableReader for the diffEngine!

This commit is contained in:
Mark DePristo 2011-08-03 18:21:18 -04:00
parent b68ed62632
commit 0ef85647f7
5 changed files with 515 additions and 395 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java
View File

@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import java.io.*;
import java.util.Collection;
import java.util.List;
import java.util.TreeMap;
@ -12,6 +13,7 @@ import java.util.TreeMap;
* Container class for GATK report tables
*/
public class GATKReport {
public static final String GATKREPORT_HEADER_PREFIX = "##:GATKReport.v";
private TreeMap<String, GATKReportTable> tables = new TreeMap<String, GATKReportTable>();
/**
@ -53,7 +55,7 @@ public class GATKReport {
String line;
while ( (line = reader.readLine()) != null ) {
if (line.startsWith("##:GATKReport.v")) {
if (line.startsWith(GATKREPORT_HEADER_PREFIX)) {
version = GATKReportVersion.fromHeader(line);
@ -169,4 +171,8 @@ public class GATKReport {
}
}
}
public Collection<GATKReportTable> getTables() {
return tables.values();
}
}

4
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportColumn.java
View File

@ -106,4 +106,8 @@ public class GATKReportColumn extends TreeMap<Object, Object> {
}
return value;
}
public String getColumnName() {
return columnName;
}
}

12
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
View File

@ -654,4 +654,16 @@ public class GATKReportTable {
public int getNumRows() {
return primaryKeyColumn.size();
}
public String getTableName() {
return tableName;
}
public String getTableDescription() {
return tableDescription;
}
public GATKReportColumns getColumns() {
return columns;
}
}

98
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java 100644
View File

@ -0,0 +1,98 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.diffengine;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportColumn;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.Map;
/**
* Class implementing diffnode reader for GATKReports
*/
public class GATKReportDiffableReader implements DiffableReader {
@Override
public String getName() { return "GATKReport"; }
@Override
public DiffElement readFromFile(File file, int maxElementsToRead) {
DiffNode root = DiffNode.rooted(file.getName());
try {
// one line reads the whole thing into memory
GATKReport report = new GATKReport(file);
for (GATKReportTable table : report.getTables() ) {
root.add(tableToNode(table, root));
}
return root.getBinding();
} catch ( Exception e ) {
return null;
}
}
private DiffNode tableToNode(GATKReportTable table, DiffNode root) {
DiffNode tableRoot = DiffNode.empty(table.getTableName(), root);
tableRoot.add("Description", table.getTableDescription());
tableRoot.add("NumberOfRows", table.getNumRows());
tableRoot.add("Version", table.getVersion());
for ( GATKReportColumn column : table.getColumns().values() ) {
DiffNode columnRoot = DiffNode.empty(column.getColumnName(), tableRoot);
columnRoot.add("Width", column.getColumnWidth());
columnRoot.add("Displayable", column.isDisplayable());
int n = 1;
for ( Object elt : column.values() ) {
String name = column.getColumnName() + n++;
columnRoot.add(name, elt.toString());
}
tableRoot.add(columnRoot);
}
return tableRoot;
}
@Override
public boolean canRead(File file) {
try {
final String HEADER = GATKReport.GATKREPORT_HEADER_PREFIX;
char[] buff = new char[HEADER.length()];
new FileReader(file).read(buff, 0, HEADER.length());
String firstLine = new String(buff);
return firstLine.startsWith(HEADER);
} catch ( IOException e ) {
return false;
}
}
}

788
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -1,394 +1,394 @@
//package org.broadinstitute.sting.gatk.walkers.varianteval;
//
//import org.broadinstitute.sting.WalkerTest;
//import org.testng.annotations.Test;
//
//import java.util.Arrays;
//import java.util.HashMap;
//import java.util.Map;
//
//public class VariantEvalIntegrationTest extends WalkerTest {
// private static String variantEvalTestDataRoot = validationDataLocation + "/VariantEval";
// private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
// private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf";
// private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.HG00625.vcf";
//
// private static String cmdRoot = "-T VariantEval" +
// " -R " + b36KGReference;
//
// private static String root = cmdRoot +
// " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
// " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
// " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
//
// private static String rootGZ = cmdRoot +
// " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
// " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
// " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz";
//
// // TODO -- I can't seem to reindex this VCF using Tabix without it causing failures. Looking into it. [EB]
// // private static String[] testsEnumerations = {root, rootGZ};
// private static String[] testsEnumerations = {root};
//
// @Test
// public void testFundamentalsCountVariantsSNPsAndIndels() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("48b8417c1f8bd74ff7b9808580abd2a2")
// );
// executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
// }
//
// @Test
// public void testFundamentalsCountVariantsSNPsAndIndelsWithNovelty() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-ST Novelty",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("86d45ecefdf5849c55b3ca8f82a3d525")
// );
// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
// }
//
// @Test
// public void testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-ST Novelty",
// "-ST Filter",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("3d18901ec1766aa2e748eac913f5ddcd")
// );
// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
// }
//
// @Test
// public void testFundamentalsCountVariantsSNPsAndIndelsWithCpG() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-ST CpG",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("677fe398643e62a10d6739d36a720a12")
// );
// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
// }
//
// @Test
// public void testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-ST FunctionalClass",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("5fb44fd7cb00941c986a9941e43e44cd")
// );
// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
// }
//
// @Test
// public void testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-ST Degeneracy",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("daaca7ef3b7313e5af217cbc6f37c9e2")
// );
// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
// }
//
// @Test
// public void testFundamentalsCountVariantsSNPsAndIndelsWithSample() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-ST Sample",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("97c466f8ffd0fcf2c30ef08669d213d9")
// );
// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
// }
//
// @Test
// public void testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-ST JexlExpression",
// "-select 'DP < 20'",
// "-selectName DepthSelect",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("df8cdfcf3d0c2fc795812c6eae6a76f8")
// );
// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
// }
//
// @Test
// public void testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-ST JexlExpression",
// "-select 'DP < 20'",
// "-selectName DepthLt20",
// "-select 'DP > 20'",
// "-selectName DepthGt20",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("c7aed12265e2b2311d17a0cc8a29f6aa")
// );
// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
// }
//
// @Test
// public void testFundamentalsCountVariantsNoCompRod() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:eval,VCF " + fundamentalTestVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("d44c8f44384189a09eea85a8e89d7299")
// );
// executeTest("testFundamentalsCountVariantsNoCompRod", spec);
// }
//
// @Test
// public void testSelect1() {
// String extraArgs = "-L 1:1-10,000,000";
// for (String tests : testsEnumerations) {
// WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
// 1, Arrays.asList("96860dedea0fa6b46c07f46b847fea42"));
// executeTestParallel("testSelect1", spec);
// }
// }
//
// @Test
// public void testVEGenotypeConcordance() {
// String vcfFile = "GenotypeConcordanceEval.vcf";
//
// WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF3 " + validationDataLocation + vcfFile + " -B:comp,VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
// 1,
// Arrays.asList("e4c981f7f5d78680c71310fc9be9a1c1"));
// executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
// }
//
// @Test
// public void testCompVsEvalAC() {
// String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
// WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("162daa5039e1965eb2423a8589339a69"));
// executeTestParallel("testCompVsEvalAC",spec);
// }
//
// private static String withSelect(String cmd, String select, String name) {
// return String.format("%s -select '%s' -selectName %s", cmd, select, name);
// }
//
// @Test
// public void testTranches() {
// String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt";
// WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("90cd98044e754b80034a9f4e6d2c55b9"));
// executeTestParallel("testTranches",spec);
// }
//
// @Test
// public void testCompOverlap() {
// String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals -B:comphapmap,vcf " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf -B:eval,vcf " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
// WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("70aa420929de7f888a6f48c2d01bbcda"));
// executeTestParallel("testCompOverlap",spec);
// }
//
// @Test
// public void testEvalTrackWithoutGenotypes() {
// String extraArgs = "-T VariantEval -R " +
// b37KGReference +
// " -L 20" +
// " -B:dbsnp,vcf " + b37dbSNP132 +
// " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
// " -noST -ST Novelty -o %s";
// WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("58fdc6c42fade3007537bb99fb3ce738"));
// executeTestParallel("testEvalTrackWithoutGenotypes",spec);
// }
//
// @Test
// public void testMultipleEvalTracksWithoutGenotypes() {
// String extraArgs = "-T VariantEval -R " + b37KGReference +
// " -L 20" +
// " -B:dbsnp,vcf " + b37dbSNP132 +
// " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
// " -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
// " -noST -ST Novelty -o %s";
// WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("34df2815d27e5e62f1694731a7e7953c"));
// executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
// }
//
// @Test
// public void testMultipleCompTracks() {
// String dbsnp = GATKDataLocation + "dbsnp_132_b37.vcf";
//
// String extraArgs = "-T VariantEval" +
// " -R " + b37KGReference +
// " -B:comp,VCF " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
// " -B:eval,VCF " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
// " -B:dbsnp,VCF " + dbsnp +
// " -L 20:10000000-10100000" +
// " -noST -noEV -ST Novelty -EV CompOverlap" +
// " -o %s";
//
// WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("20332902ae36a84b2fd80405410815f1"));
// executeTestParallel("testMultipleCompTracks",spec);
// }
//
// @Test
// public void testPerSampleAndSubsettedSampleHaveSameResults() {
// String md5 = "9d61f6e2c8592dcf616712a2c587b2af";
//
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestSNPsVCF,
// "-noEV",
// "-EV CompOverlap",
// "-sn HG00625",
// "-noST",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList(md5)
// );
// executeTestParallel("testPerSampleAndSubsettedSampleHaveSameResults-subset", spec);
//
// WalkerTestSpec spec2 = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF,
// "-noEV",
// "-EV CompOverlap",
// "-noST",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList(md5)
// );
// executeTestParallel("testPerSampleAndSubsettedSampleHaveSameResults-onesample", spec2);
// }
//
//
// @Test
// public void testAlleleCountStrat() {
// WalkerTestSpec spec = new WalkerTestSpec(
// buildCommandLine(
// "-T VariantEval",
// "-R " + b37KGReference,
// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
// "-B:eval,VCF " + fundamentalTestSNPsVCF,
// "-noEV",
// "-EV CountVariants",
// "-noST",
// "-ST AlleleCount",
// "-BTI eval",
// "-o %s"
// ),
// 1,
// Arrays.asList("bf324e4c87fe0d21170fcd2a67a20371")
// );
// executeTest("testAlleleCountStrat", spec);
// }
//}
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
public class VariantEvalIntegrationTest extends WalkerTest {
private static String variantEvalTestDataRoot = validationDataLocation + "/VariantEval";
private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf";
private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.HG00625.vcf";
private static String cmdRoot = "-T VariantEval" +
" -R " + b36KGReference;
private static String root = cmdRoot +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
" -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
" -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
private static String rootGZ = cmdRoot +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" +
" -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" +
" -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz";
// TODO -- I can't seem to reindex this VCF using Tabix without it causing failures. Looking into it. [EB]
// private static String[] testsEnumerations = {root, rootGZ};
private static String[] testsEnumerations = {root};
@Test
public void testFundamentalsCountVariantsSNPsAndIndels() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("48b8417c1f8bd74ff7b9808580abd2a2")
);
executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
}
@Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithNovelty() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST Novelty",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("86d45ecefdf5849c55b3ca8f82a3d525")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
}
@Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST Novelty",
"-ST Filter",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("3d18901ec1766aa2e748eac913f5ddcd")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
}
@Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithCpG() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST CpG",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("677fe398643e62a10d6739d36a720a12")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
}
@Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST FunctionalClass",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("5fb44fd7cb00941c986a9941e43e44cd")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
}
@Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST Degeneracy",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("daaca7ef3b7313e5af217cbc6f37c9e2")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
}
@Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithSample() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST Sample",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("97c466f8ffd0fcf2c30ef08669d213d9")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
}
@Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST JexlExpression",
"-select 'DP < 20'",
"-selectName DepthSelect",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("df8cdfcf3d0c2fc795812c6eae6a76f8")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
}
@Test
public void testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST JexlExpression",
"-select 'DP < 20'",
"-selectName DepthLt20",
"-select 'DP > 20'",
"-selectName DepthGt20",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("c7aed12265e2b2311d17a0cc8a29f6aa")
);
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
}
@Test
public void testFundamentalsCountVariantsNoCompRod() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:eval,VCF " + fundamentalTestVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("d44c8f44384189a09eea85a8e89d7299")
);
executeTest("testFundamentalsCountVariantsNoCompRod", spec);
}
@Test
public void testSelect1() {
String extraArgs = "-L 1:1-10,000,000";
for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
1, Arrays.asList("96860dedea0fa6b46c07f46b847fea42"));
executeTestParallel("testSelect1", spec);
}
}
@Test
public void testVEGenotypeConcordance() {
String vcfFile = "GenotypeConcordanceEval.vcf";
WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF3 " + validationDataLocation + vcfFile + " -B:comp,VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s",
1,
Arrays.asList("e4c981f7f5d78680c71310fc9be9a1c1"));
executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec);
}
@Test
public void testCompVsEvalAC() {
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("162daa5039e1965eb2423a8589339a69"));
executeTestParallel("testCompVsEvalAC",spec);
}
private static String withSelect(String cmd, String select, String name) {
return String.format("%s -select '%s' -selectName %s", cmd, select, name);
}
@Test
public void testTranches() {
String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("90cd98044e754b80034a9f4e6d2c55b9"));
executeTestParallel("testTranches",spec);
}
@Test
public void testCompOverlap() {
String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals -B:comphapmap,vcf " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf -B:eval,vcf " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("70aa420929de7f888a6f48c2d01bbcda"));
executeTestParallel("testCompOverlap",spec);
}
@Test
public void testEvalTrackWithoutGenotypes() {
String extraArgs = "-T VariantEval -R " +
b37KGReference +
" -L 20" +
" -B:dbsnp,vcf " + b37dbSNP132 +
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("58fdc6c42fade3007537bb99fb3ce738"));
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
}
@Test
public void testMultipleEvalTracksWithoutGenotypes() {
String extraArgs = "-T VariantEval -R " + b37KGReference +
" -L 20" +
" -B:dbsnp,vcf " + b37dbSNP132 +
" -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
" -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
" -noST -ST Novelty -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("34df2815d27e5e62f1694731a7e7953c"));
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
}
@Test
public void testMultipleCompTracks() {
String dbsnp = GATKDataLocation + "dbsnp_132_b37.vcf";
String extraArgs = "-T VariantEval" +
" -R " + b37KGReference +
" -B:comp,VCF " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" +
" -B:eval,VCF " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" +
" -B:dbsnp,VCF " + dbsnp +
" -L 20:10000000-10100000" +
" -noST -noEV -ST Novelty -EV CompOverlap" +
" -o %s";
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("20332902ae36a84b2fd80405410815f1"));
executeTestParallel("testMultipleCompTracks",spec);
}
@Test
public void testPerSampleAndSubsettedSampleHaveSameResults() {
String md5 = "9d61f6e2c8592dcf616712a2c587b2af";
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CompOverlap",
"-sn HG00625",
"-noST",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList(md5)
);
executeTestParallel("testPerSampleAndSubsettedSampleHaveSameResults-subset", spec);
WalkerTestSpec spec2 = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF,
"-noEV",
"-EV CompOverlap",
"-noST",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList(md5)
);
executeTestParallel("testPerSampleAndSubsettedSampleHaveSameResults-onesample", spec2);
}
@Test
public void testAlleleCountStrat() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf",
"-B:eval,VCF " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST AlleleCount",
"-BTI eval",
"-o %s"
),
1,
Arrays.asList("bf324e4c87fe0d21170fcd2a67a20371")
);
executeTest("testAlleleCountStrat", spec);
}
}