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Merge pull request #145 from broadinstitute/eb_various_minor_fixes 

Eb various minor fixes
This commit is contained in:
Mark DePristo 2013-04-05 06:06:54 -07:00
parent 03811b4274 6253ba164e
commit 56f4529ef3
7 changed files with 66 additions and 20 deletions
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8
protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
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@ -47,6 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
import java.util.Arrays;
@ -106,6 +107,13 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
executeTest("test filter sites not in mask", spec3);
}
@Test
public void testIllegalFilterName() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName 'foo < foo' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
UserException.class);
executeTest("test illegal filter name", spec);
}
@Test
public void testFilter1() {

26
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
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@ -242,6 +242,32 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testRemoveMLE--" + testFile, spec);
}
@Test
public void testKeepOriginalAC() {
String testFile = privateTestDir + "vcfexample.loseAlleleInSelection.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants --keepOriginalAC -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("ad7e8b25e431a3229a78cec063876559")
);
executeTest("testKeepOriginalAC--" + testFile, spec);
}
@Test
public void testKeepOriginalACAndENV() {
String testFile = privateTestDir + "vcfexample.loseAlleleInSelection.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants --keepOriginalAC -env -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("e9b8292212545684cdb163423329ee7e")
);
executeTest("testKeepOriginalACAndENV--" + testFile, spec);
}
@Test
public void testMultipleRecordsAtOnePosition() {
String testFile = privateTestDir + "selectVariants.onePosition.vcf";

8
public/java/src/org/broadinstitute/sting/commandline/ArgumentMatch.java
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@ -276,10 +276,10 @@ public class ArgumentMatch implements Iterable<ArgumentMatch> {
* @return A collection of the string representation of these value.
*/
public List<ArgumentMatchValue> values() {
List<ArgumentMatchValue> values = new ArrayList<ArgumentMatchValue>();
for( ArgumentMatchSite site: sites.keySet() ) {
if( sites.get(site) != null )
values.addAll(sites.get(site));
final List<ArgumentMatchValue> values = new ArrayList<ArgumentMatchValue>();
for ( final List<ArgumentMatchValue> siteValue : sites.values() ) {
if ( siteValue != null )
values.addAll(siteValue);
}
return values;
}

22
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
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@ -186,18 +186,22 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
if ( clusterWindow > 0 )
hInfo.add(new VCFFilterHeaderLine(CLUSTERED_SNP_FILTER_NAME, "SNPs found in clusters"));
for ( VariantContextUtils.JexlVCMatchExp exp : filterExps )
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps )
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
if ( genotypeFilterExps.size() > 0 )
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
if ( mask.isBound() ) {
if (filterRecordsNotInMask)
hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Doesn't overlap a user-input mask"));
else hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));
try {
for ( VariantContextUtils.JexlVCMatchExp exp : filterExps )
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps )
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
if ( mask.isBound() ) {
if (filterRecordsNotInMask)
hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Doesn't overlap a user-input mask"));
else hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));
}
} catch (IllegalArgumentException e) {
throw new UserException.BadInput(e.getMessage());
}
writer.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));

20
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -406,8 +406,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
headerLines.add(new VCFHeaderLine("source", "SelectVariants"));
if (KEEP_ORIGINAL_CHR_COUNTS) {
headerLines.add(new VCFInfoHeaderLine("AC_Orig", 1, VCFHeaderLineType.Integer, "Original AC"));
headerLines.add(new VCFInfoHeaderLine("AF_Orig", 1, VCFHeaderLineType.Float, "Original AF"));
headerLines.add(new VCFInfoHeaderLine("AC_Orig", VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Original AC"));
headerLines.add(new VCFInfoHeaderLine("AF_Orig", VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Original AF"));
headerLines.add(new VCFInfoHeaderLine("AN_Orig", 1, VCFHeaderLineType.Integer, "Original AN"));
}
headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions));
@ -670,7 +670,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
GenotypesContext newGC = sub.getGenotypes();
// if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs and AD (because they are no longer accurate)
if ( vc.getAlleles().size() != sub.getAlleles().size() )
final boolean lostAllelesInSelection = vc.getAlleles().size() != sub.getAlleles().size();
if ( lostAllelesInSelection )
newGC = GATKVariantContextUtils.stripPLsAndAD(sub.getGenotypes());
// if we have fewer samples in the selected VC than in the original VC, we need to strip out the MLE tags
@ -697,15 +698,22 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
builder.genotypes(newGC);
addAnnotations(builder, sub);
addAnnotations(builder, sub, lostAllelesInSelection);
return builder.make();
}
private void addAnnotations(final VariantContextBuilder builder, final VariantContext originalVC) {
/*
* Add annotations to the new VC
*
* @param builder the new VC to annotate
* @param originalVC the original -- but post-selection -- VC
* @param lostAllelesInSelection true if the original (pre-selection) VC has more alleles than the new one
*/
private void addAnnotations(final VariantContextBuilder builder, final VariantContext originalVC, final boolean lostAllelesInSelection) {
if ( fullyDecode ) return; // TODO -- annotations are broken with fully decoded data
if (KEEP_ORIGINAL_CHR_COUNTS) {
if ( KEEP_ORIGINAL_CHR_COUNTS && !lostAllelesInSelection ) {
if ( originalVC.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) )
builder.attribute("AC_Orig", originalVC.getAttribute(VCFConstants.ALLELE_COUNT_KEY));
if ( originalVC.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) )

BIN
settings/repository/org.broadinstitute/variant-1.85.1357.jar → settings/repository/org.broadinstitute/variant-1.88.1401.jar
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Binary file not shown.

2
settings/repository/org.broadinstitute/variant-1.85.1357.xml → settings/repository/org.broadinstitute/variant-1.88.1401.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broadinstitute" module="variant" revision="1.85.1357" status="integration" />
<info organisation="org.broadinstitute" module="variant" revision="1.88.1401" status="integration" />
</ivy-module>