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Added annotation of INCORRECT SNP-based aa annotations in case of MNPdependentAA:true 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5576 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-04-05 02:46:45 +00:00
parent bb6a30611c
commit 5eccc7e528
1 changed files with 11 additions and 1 deletions
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12
java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
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@ -605,6 +605,7 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
private CodonFunction codonFunc;
private String proteinCoordStr;
private boolean MNPdependentAA;
private String originalAA;
public SingleCodonAnnotationsForAllele(String variantCodon, String refCodon, AminoAcid refAA, int codonIndex) {
this.codonFunc = new CodonFunction(variantCodon, refCodon, refAA);
@ -615,15 +616,24 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
throw new ReviewedStingException("codonFunc.variantCodon.length() != refCodonLength, but ALREADY checked that they're both 3");
this.MNPdependentAA = true;
this.originalAA = "(";
for (int i = 0; i < refCodonLength; i++) {
// Take [0,i-1] and [i+1, end] from refCodon, and i from variantCodon:
String singleBaseChangeCodon = refCodon.substring(0, i) + variantCodon.substring(i, i+1) + refCodon.substring(i+1, refCodonLength);
CodonFunction singleBaseChangeCodonFunc = new CodonFunction(singleBaseChangeCodon, refCodon, refAA);
if (singleBaseChangeCodonFunc.variantAA.equals(codonFunc.variantAA)) {
this.MNPdependentAA = false;
this.originalAA = "";
break;
}
this.originalAA = this.originalAA + "" + singleBaseChangeCodonFunc.variantAA.getLetter();
if (i < refCodonLength - 1)
this.originalAA = this.originalAA + ",";
}
if (this.MNPdependentAA)
this.originalAA = this.originalAA + ")";
}
private static class CodonFunction {
@ -668,7 +678,7 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
sb.append(REFSEQ_CHANGES_AA).append(ASSIGNMENT).append(codonFunc.changesAA).append(CODON_INFO_DELIM);
sb.append(REFSEQ_FUNCTIONAL_CLASS).append(ASSIGNMENT).append(codonFunc.functionalClass).append(CODON_INFO_DELIM);
sb.append(REFSEQ_PROTEIN_COORD_DESCRIPTION).append(ASSIGNMENT).append(proteinCoordStr).append(CODON_INFO_DELIM);
sb.append(MNP_DEPENDENT_AA).append(ASSIGNMENT).append(MNPdependentAA);
sb.append(MNP_DEPENDENT_AA).append(ASSIGNMENT).append(MNPdependentAA).append(originalAA);
sb.append(ALLELE_END);
return sb.toString();