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Merge pull request #132 from broadinstitute/gda_filter_unmasked_sites 

Added small feature to VariantFiltration to filter sites outside of a gi...
This commit is contained in:
Eric Banks 2013-03-31 06:27:26 -07:00
parent 4f828ca86f 9686e91a51
commit 7dd58f671f
2 changed files with 26 additions and 4 deletions
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9
protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -98,6 +98,15 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
executeTest("test mask extend", spec3);
}
@Test
public void testMaskReversed() {
WalkerTestSpec spec3 = new WalkerTestSpec(
baseTestString() + " -maskName outsideGoodSites -filterNotInMask --mask:BED " + privateTestDir + "goodMask.bed --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("e65d27c13953fc3a77dcad27a4357786"));
executeTest("test filter sites not in mask", spec3);
}
@Test
public void testFilter1() {
WalkerTestSpec spec = new WalkerTestSpec(

21
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
View File

@ -87,9 +87,10 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
/**
* Any variant which overlaps entries from the provided mask rod will be filtered.
* Any variant which overlaps entries from the provided mask rod will be filtered. If the user wants logic to be reversed,
* i.e. filter variants that do not overlap with provided mask, then argument -filterNotInMask can be used.
*/
@Input(fullName="mask", doc="Input ROD mask", required=false)
@Input(fullName="mask", shortName="mask", doc="Input ROD mask", required=false)
public RodBinding<Feature> mask;
@Output(doc="File to which variants should be written")
@ -140,6 +141,14 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
@Argument(fullName="maskName", shortName="maskName", doc="The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call", required=false)
protected String MASK_NAME = "Mask";
/**
* By default, if the -mask argument is used, any variant falling in a mask will be filtered.
* If this argument is used, logic is reversed, and variants falling outside a given mask will be filtered.
* Use case is, for example, if we have an interval list or BED file with "good" sites.
*/
@Argument(fullName="filterNotInMask", shortName="filterNotInMask", doc="Filter records NOT in given input mask.", required=false)
protected boolean filterRecordsNotInMask = false;
/**
* By default, if JEXL cannot evaluate your expression for a particular record because one of the annotations is not present, the whole expression evaluates as PASSing.
* Use this argument to have it evaluate as failing filters instead for these cases.
@ -186,7 +195,9 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
if ( mask.isBound() ) {
hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));
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"));
}
writer.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
@ -199,6 +210,8 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
if ( MASK_EXTEND < 0 )
throw new UserException.BadArgumentValue("maskExtension", "negative values are not allowed");
if (filterRecordsNotInMask && !mask.isBound())
throw new UserException.BadArgumentValue("filterNotInMask","argument not allowed if mask argument is not provided");
filterExps = VariantContextUtils.initializeMatchExps(FILTER_NAMES, FILTER_EXPS);
genotypeFilterExps = VariantContextUtils.initializeMatchExps(GENOTYPE_FILTER_NAMES, GENOTYPE_FILTER_EXPS);
@ -223,7 +236,7 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
// is there a SNP mask present?
boolean hasMask = tracker.hasValues(mask);
boolean hasMask = (tracker.hasValues(mask) && !filterRecordsNotInMask) || (filterRecordsNotInMask && !tracker.hasValues(mask));
if ( hasMask )
previousMaskPosition = ref.getLocus(); // multi-base masks will get triggered over all bases of the mask