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Simple change to allow a list of samples or regular expressions to be provided in a text file (one line per sample). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4074 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-08-21 00:01:48 +00:00
parent 165dc6d3b0
commit 121b4f23b6
2 changed files with 34 additions and 7 deletions
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38
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -40,6 +40,8 @@ import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
@ -47,6 +49,8 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFWriterImpl;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.io.File;
import java.io.FileNotFoundException;
/**
* Takes a VCF file, selects variants based on sample(s) in which it was found and/or on various annotation criteria,
@ -54,7 +58,7 @@ import java.util.regex.Pattern;
*/
@Requires(value={},referenceMetaData=@RMD(name="variant", type=ReferenceOrderedDatum.class))
public class SelectVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="sample", shortName="sn", doc="Sample(s) to include. Can be a single sample, specified multiple times for many samples, or a regular expression to select many samples.", required=false)
@Argument(fullName="sample", shortName="sn", doc="Sample(s) to include. Can be a single sample, specified multiple times for many samples, a file containing sample names, a regular expression to select many samples, or any combination thereof.", required=false)
public Set<String> SAMPLE_EXPRESSIONS;
@Argument(shortName="select", doc="One or more criteria to use when selecting the data. Evaluated *after* the specified samples are extracted and the INFO-field annotations are updated.", required=false)
@ -88,14 +92,36 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
if (SAMPLE_EXPRESSIONS != null) {
// Let's first assume that the values in SAMPLE_EXPRESSIONS are literal sample names and not regular
// Let's first go through the list and see if we were given any files. We'll add every entry in the file to our
// sample list set, and treat the entries as if they had been specified on the command line.
Set<String> samplesFromFiles = new HashSet<String>();
for (String SAMPLE_EXPRESSION : SAMPLE_EXPRESSIONS) {
File sampleFile = new File(SAMPLE_EXPRESSION);
try {
XReadLines reader = new XReadLines(sampleFile);
List<String> lines = reader.readLines();
for (String line : lines) {
samplesFromFiles.add(line);
}
} catch (FileNotFoundException e) {
// ignore exception
}
}
SAMPLE_EXPRESSIONS.addAll(samplesFromFiles);
// Let's now assume that the values in SAMPLE_EXPRESSIONS are literal sample names and not regular
// expressions. Extract those samples specifically so we don't make the mistake of selecting more
// than what the user really wants.
for (String SAMPLE_EXPRESSION : SAMPLE_EXPRESSIONS) {
if (vcfSamples.contains(SAMPLE_EXPRESSION)) {
samples.add(SAMPLE_EXPRESSION);
} else {
possibleSampleRegexs.add(SAMPLE_EXPRESSION);
if (!(new File(SAMPLE_EXPRESSION).exists())) {
if (vcfSamples.contains(SAMPLE_EXPRESSION)) {
samples.add(SAMPLE_EXPRESSION);
} else {
possibleSampleRegexs.add(SAMPLE_EXPRESSION);
}
}
}

3
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -13,9 +13,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
@Test
public void testComplexSelection() {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -sn '[CDEH]' -env -ef -select 'AF < 0.2' -B variant,VCF," + testfile),
baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'AF < 0.2' -B variant,VCF," + testfile),
1,
Arrays.asList("3a15628b5980031c629c0c33e7e60b40")
);