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Removed HAPLOTYPE_STRAND_COLUMN; Previously, GenomicAnnotation allowed a user to specify the strand of the haplotypeAlternate, and would reverseComplement the haplotypeAlternate if HAPLOTYPE_STRAND_COLUMN was "-". The new specification does not allow this functionality, and instead requires both the reference and the alternate haplotypes to be on the + strand (as in VCF format). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4443 348d0f76-0448-11de-a6fe-93d51630548a
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scalvo 2010-10-06 20:37:41 +00:00
parent ca5db821ce
commit b5c127e643
1 changed files with 0 additions and 16 deletions
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16
java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
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@ -56,7 +56,6 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
public static final String END_COLUMN = "end";
public static final String HAPLOTYPE_REFERENCE_COLUMN = "haplotypeReference";
public static final String HAPLOTYPE_ALTERNATE_COLUMN = "haplotypeAlternate";
public static final String HAPLOTYPE_STRAND_COLUMN = "haplotypeStrand";
public static final String NUM_MATCHES_SPECIAL_INFO_FIELD = "numMatchingRecords";
@ -137,18 +136,6 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
throw new UserException.MalformedFile("File associated with " + vc.getName() + " contains record [" + vc + "] contains " + alternateAlleles.size() + " alternate alleles. GenomicAnnotion currently only supports annotating 1 alternate allele.");
}
boolean positiveStrand = true; //if HAPLOTYPE_STRAND_COLUMN isn't specified, assume positive strand.
String hapStrandValue = annotationsForRecord.get( generateInfoFieldKey(name, HAPLOTYPE_STRAND_COLUMN) );
if(hapStrandValue != null ) {
hapStrandValue = hapStrandValue.trim().toLowerCase();
if(hapStrandValue.equals("-") || hapStrandValue.equals("r")) {
positiveStrand = false;
} else if(!hapStrandValue.equals("+") && !hapStrandValue.equals("f")) {
throw new UserException.MalformedFile("Record (" + gatkFeature.getUnderlyingObject() + ") in " + name + " has an invalid value for " + HAPLOTYPE_STRAND_COLUMN + ". This value is: \"" + hapStrandValue + "\"");
}
}
Allele vcAlt;
if(alternateAlleles.isEmpty()) {
vcAlt = vc.getReference();
@ -158,9 +145,6 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
boolean matchFound = false;
for(String hapAlt : hapAltValue.split("[,\\\\/:|]")) {
if(!positiveStrand) {
hapAlt = new String(BaseUtils.simpleReverseComplement(hapAlt.getBytes()));
}
if(!hapAlt.isEmpty() && vcAlt.basesMatch(hapAlt)) {
matchFound = true;