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gatk-3.8
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1. Alignability mask returns null when not available. 

2. --list now prints out the available classes/groups too.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3072 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-24 20:49:07 +00:00
parent 06a212e612
commit 3176715c74
2 changed files with 12 additions and 20 deletions
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19
java/src/org/broadinstitute/sting/gatk/walkers/annotator/Alignability.java
View File

@ -20,17 +20,14 @@ public class Alignability implements InfoFieldAnnotation {
VariantContext vc) VariantContext vc)
{ {
TabularROD record = (TabularROD)(tracker.lookup("alignability", null)); TabularROD record = (TabularROD)(tracker.lookup("alignability", null));
int value; if (record == null)
if (record == null) { value = 3; } return null;
else
{ if (record.get("alignability") == null)
if (record.get("alignability") == null) throw new RuntimeException("ERROR: alignability column not defined in alignability input.\n");
{
throw new RuntimeException("ERROR: alignability column not defined in alignability input.\n"); int value = Integer.parseInt(record.get("alignability"));
}
value = Integer.parseInt(record.get("alignability"));
}
Map<String, Object> map = new HashMap<String, Object>(); Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyName(), String.format("%d", value)); map.put(getKeyName(), String.format("%d", value));
return map; return map;

13
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -8,7 +8,6 @@ import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.vcf.*; import org.broadinstitute.sting.utils.genotype.vcf.*;
import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import java.util.*; import java.util.*;
@ -54,6 +53,10 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
for (int i = 0; i < genotypeAnnotationClasses.size(); i++) for (int i = 0; i < genotypeAnnotationClasses.size(); i++)
out.println("\t" + genotypeAnnotationClasses.get(i).getSimpleName()); out.println("\t" + genotypeAnnotationClasses.get(i).getSimpleName());
out.println(); out.println();
out.println("\nAvailable classes/groups of annotations:");
for ( Class c : PackageUtils.getInterfacesExtendingInterface(AnnotationType.class) )
out.println("\t" + c.getSimpleName());
out.println();
System.exit(0); System.exit(0);
} }
@ -168,12 +171,4 @@ public class VariantAnnotator extends LocusWalker<Integer, Integer> {
vcfWriter.close(); vcfWriter.close();
} }
public static Genotype getFirstVariant(char ref, List<Genotype> genotypes) {
for ( Genotype g : genotypes ) {
if ( g.isVariant(ref) )
return g;
}
return null;
}
} }