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Modified SampleFilter to allow for multiple samples to be given. AminoAcidTransition now turns on when you give VariantEval the right commands. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3812 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-07-16 21:27:32 +00:00
parent b0fc42906e
commit 75bea4881a
2 changed files with 8 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java
View File

@ -30,12 +30,14 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import java.util.Set;
public class SampleFilter implements SamRecordFilter { public class SampleFilter implements SamRecordFilter {
@Argument(fullName = "sample_to_keep", shortName = "goodSM", doc="The name of the sample to keep, filtering out all others", required=true) @Argument(fullName = "sample_to_keep", shortName = "goodSM", doc="The name of the sample(s) to keep, filtering out all others", required=true)
private String SAMPLE_TO_KEEP = null; private Set SAMPLES_TO_KEEP = null;
public boolean filterOut( final SAMRecord read ) { public boolean filterOut( final SAMRecord read ) {
final SAMReadGroupRecord readGroup = read.getReadGroup(); final SAMReadGroupRecord readGroup = read.getReadGroup();
return !( readGroup != null && readGroup.getSample().equals( SAMPLE_TO_KEEP ) ); return !( readGroup != null && SAMPLES_TO_KEEP.contains(readGroup.getSample()) );
} }
} }

4
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java
View File

@ -127,10 +127,12 @@ public class AminoAcidTransition extends VariantEvaluator {
private String infoKey; private String infoKey;
private String infoValueSplit; private String infoValueSplit;
private boolean useCodons; private boolean useCodons;
private boolean enabled;
private AminoAcidTable lookup; private AminoAcidTable lookup;
public AminoAcidTransition(VariantEvalWalker parent) { public AminoAcidTransition(VariantEvalWalker parent) {
super(parent); super(parent);
enabled = parent.aminoAcidTransitionKey != null;
getParsingInformation(parent); getParsingInformation(parent);
lookup = new AminoAcidTable(); lookup = new AminoAcidTable();
acidTable = new AminoAcidTiTvTable(); acidTable = new AminoAcidTiTvTable();
@ -160,7 +162,7 @@ public class AminoAcidTransition extends VariantEvaluator {
} }
public boolean enabled() { public boolean enabled() {
return false; return enabled;
} }
public String toString() { public String toString() {