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AC strat now checks if evals will be merged before throwing an error on multiple eval files. 

Minor tweaks to WGP script based on new recal VCF format.
This commit is contained in:
Khalid Shakir 2012-04-19 16:08:55 -04:00
parent 3fa9089085
commit df5dd841af
2 changed files with 63 additions and 18 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
View File

@ -20,10 +20,8 @@ import java.util.*;
public class AlleleCount extends VariantStratifier {
@Override
public void initialize() {
List<RodBinding<VariantContext>> evals = getVariantEvalWalker().getEvals();
// we can only work with a single eval VCF, and it must have genotypes
if ( evals.size() != 1 )
if ( getVariantEvalWalker().getEvals().size() != 1 && !getVariantEvalWalker().mergeEvals )
throw new UserException.BadArgumentValue("AlleleCount", "AlleleCount stratification only works with a single eval vcf");
// There are 2 x n sample chromosomes for diploids

77
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -34,6 +34,8 @@ 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 fundamentalTestSNPsSplit1of2VCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.split_1_of_2.vcf";
private static String fundamentalTestSNPsSplit2of2VCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.split_2_of_2.vcf";
private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.NA12045.vcf";
private static String cmdRoot = "-T VariantEval" +
@ -437,24 +439,69 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testAlleleCountStrat() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"--dbsnp " + b37dbSNP132,
"--eval " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST AlleleCount",
"-L " + fundamentalTestSNPsVCF,
"-o %s"
),
1,
Arrays.asList("1198bfea6183bd43219071a84c79a386")
);
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"--dbsnp " + b37dbSNP132,
"--eval " + fundamentalTestSNPsVCF,
"-noEV",
"-EV CountVariants",
"-noST",
"-ST AlleleCount",
"-L " + fundamentalTestSNPsVCF,
"-o %s"
),
1,
Arrays.asList("1198bfea6183bd43219071a84c79a386")
);
executeTest("testAlleleCountStrat", spec);
}
@Test
public void testMultipleEvalTracksAlleleCountWithMerge() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"--dbsnp " + b37dbSNP132,
"--eval " + fundamentalTestSNPsSplit1of2VCF,
"--eval " + fundamentalTestSNPsSplit2of2VCF,
"--mergeEvals",
"-noEV",
"-EV CountVariants",
"-noST",
"-ST AlleleCount",
"-L " + fundamentalTestSNPsVCF,
"-o %s"
),
1,
Arrays.asList("1198bfea6183bd43219071a84c79a386")
);
executeTest("testMultipleEvalTracksAlleleCountWithMerge", spec);
}
@Test
public void testMultipleEvalTracksAlleleCountWithoutMerge() {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T VariantEval",
"-R " + b37KGReference,
"--dbsnp " + b37dbSNP132,
"--eval " + fundamentalTestSNPsSplit1of2VCF,
"--eval " + fundamentalTestSNPsSplit2of2VCF,
//"--mergeEvals", No merge with AC strat ==> error
"-noEV",
"-EV CountVariants",
"-noST",
"-ST AlleleCount",
"-L " + fundamentalTestSNPsVCF
),
0,
UserException.class
);
executeTest("testMultipleEvalTracksAlleleCountWithoutMerge", spec);
}
@Test
public void testIntervalStrat() {
WalkerTestSpec spec = new WalkerTestSpec(