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VariantFiltration now accepts any number of --name --filter expressions, and annotates the VCF file with each name that matches. Very useful 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2732 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-01-29 12:13:08 +00:00
parent 01e73fc39e
commit 5aaf4e6434
2 changed files with 43 additions and 14 deletions
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49
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
View File

@ -18,9 +18,9 @@ import org.apache.commons.jexl.*;
@Requires(value={},referenceMetaData=@RMD(name="variant",type= RodVCF.class))
public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
@Argument(fullName="filterExpression", shortName="filter", doc="Expression used with INFO fields to filter (see wiki docs for more info)", required=false)
protected String FILTER_STRING = null;
protected String[] FILTER_STRINGS = new String[]{null};
@Argument(fullName="filterName", shortName="filterName", doc="The text to put in the FILTER field if a filter expression is provided and a variant call matches", required=false)
protected String FILTER_NAME = "GATK_filter";
protected String[] FILTER_NAMES = new String[]{"GATK_filter"};
@Argument(fullName="clusterSize", shortName="cluster", doc="The number of SNPs which make up a cluster (see also --clusterWindowSize)", required=false)
protected Integer clusterSize = 3;
@ -32,12 +32,23 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
public static final String CLUSTERED_SNP_FILTER_NAME = "SnpCluster";
private VCFWriter writer = null;
private ClusteredSnps clusteredSNPs = null;
private Expression filterExpression = null;
class FilterExp {
String name;
String expStr;
Expression exp;
public FilterExp(String name, String str, Expression exp) {
this.name = name;
this.expStr = str;
this.exp = exp;
}
}
private List<FilterExp> filterExpressions = new ArrayList<FilterExp>();
// the structures necessary to initialize and maintain a windowed context
private VariantContextWindow variantContextWindow;
@ -54,8 +65,11 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( clusterWindow > 0 )
hInfo.add(new VCFFilterHeaderLine(CLUSTERED_SNP_FILTER_NAME, "SNPs found in clusters"));
if ( filterExpression != null )
hInfo.add(new VCFFilterHeaderLine(FILTER_NAME, FILTER_STRING));
for ( FilterExp exp : filterExpressions ) {
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.expStr));
}
List<ReferenceOrderedDataSource> dataSources = getToolkit().getRodDataSources();
for ( ReferenceOrderedDataSource source : dataSources ) {
if ( source.getReferenceOrderedData().getName().equals("mask") ) {
@ -72,11 +86,18 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( clusterWindow > 0 )
clusteredSNPs = new ClusteredSnps(clusterSize, clusterWindow);
try {
if ( FILTER_STRING != null )
filterExpression = ExpressionFactory.createExpression(FILTER_STRING);
} catch (Exception e) {
throw new StingException("Invalid expression used (" + FILTER_STRING + "). Please see the JEXL docs for correct syntax.");
if ( FILTER_NAMES.length != FILTER_STRINGS.length )
throw new StingException("Inconsistent number of provided filter names and expressions.");
for ( int i = 0; i < FILTER_NAMES.length; i++ ) {
if ( FILTER_STRINGS[i] != null ) {
try {
Expression filterExpression = ExpressionFactory.createExpression(FILTER_STRINGS[i]);
filterExpressions.add(new FilterExp(FILTER_NAMES[i], FILTER_STRINGS[i], filterExpression));
} catch (Exception e) {
throw new StingException("Invalid expression used (" + FILTER_STRINGS[i] + "). Please see the JEXL docs for correct syntax.");
}
}
}
}
@ -134,7 +155,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( clusteredSNPs != null && clusteredSNPs.filter(variantContextWindow) )
addFilter(filterString, CLUSTERED_SNP_FILTER_NAME);
if ( filterExpression != null ) {
for ( FilterExp exp : filterExpressions ) {
Map<String, String> infoMap = new HashMap<String, String>(context.second.mCurrentRecord.getInfoValues());
infoMap.put("QUAL", String.valueOf(context.second.mCurrentRecord.getQual()));
@ -142,8 +163,8 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
jContext.setVars(infoMap);
try {
if ( (Boolean)filterExpression.evaluate(jContext) )
addFilter(filterString, FILTER_NAME);
if ( (Boolean)exp.exp.evaluate(jContext) )
addFilter(filterString, exp.name);
} catch (Exception e) {
throw new StingException(e.getMessage());
}

8
java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -51,4 +51,12 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
Arrays.asList("18ef67575a76c2be74af8bd8b9fdf86e"));
executeTest("test filter #2", spec);
}
@Test
public void testFilterWithSeparateNames() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 70.0' --filterName FSF -filter 'FisherStrand == 1.4' -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("7de66cac85cfe8a70219e51a5f6c251c"));
executeTest("test filter with separate names #2", spec);
}
}