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Now output bases and qhat and qstar into the GFF. 

Quals coming soon (four-base)

QHAT  : Most likely alt allele freq (unconstrained by number of chromosomes).
QSTAR : Most likely alt allele freq (constrained by number of chromosomes).





git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@402 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-04-14 15:23:00 +00:00
parent dafdff1974
commit 961dbbd4ef
2 changed files with 19 additions and 10 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
View File

@ -356,7 +356,9 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
lodBestVsNextBest,
bestMixtures[0].posterior,
posterior_null_hyp,
depth);
depth,
new String(bases),
quals);
return alleleFreq;
}

25
java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
View File

@ -19,10 +19,12 @@ public class AlleleFrequencyEstimate {
public double pRef;
public int depth;
public String notes;
public String bases;
public double[][] quals;
GenomeLoc l;
public AlleleFrequencyEstimate(GenomeLoc location, char ref, char alt, int N, double qhat, double qstar, double lodVsRef, double lodVsNextBest, double pBest, double pRef, int depth)
public AlleleFrequencyEstimate(GenomeLoc location, char ref, char alt, int N, double qhat, double qstar, double lodVsRef, double lodVsNextBest, double pBest, double pRef, int depth, String bases, double[][] quals)
{
this.location = location;
this.ref = ref;
@ -34,6 +36,8 @@ public class AlleleFrequencyEstimate {
this.lodVsNextBest = lodVsNextBest;
this.depth = depth;
this.notes = "";
this.bases = bases;
this.quals = quals;
}
/** Return the most likely genotype. */
@ -67,16 +71,19 @@ public class AlleleFrequencyEstimate {
location.getStart(),
location.getStart(),
lodVsRef);
s += String.format("REF %c\t;\t", ref);
s += String.format("ALT %c\t;\t", alt);
s += String.format("FREQ %f\t;\t;", qstar);
s += String.format("DEPTH %d\t;\t", depth);
s += String.format("LODvsREF %f\t;\t", lodVsRef);
s += String.format("LODvsNEXTBEST %f\t;\t", lodVsNextBest);
s += String.format("\t;\tREF %c", ref);
s += String.format("\t;\tALT %c", alt);
s += String.format("\t;\tFREQ %f", qstar);
s += String.format("\t;\tDEPTH %d", depth);
s += String.format("\t;\tLODvsREF %f", lodVsRef);
s += String.format("\t;\tLODvsNEXTBEST %f", lodVsNextBest);
s += String.format("\t;\tQHAT %f", qhat);
s += String.format("\t;\tQSTAR %f", qstar);
s += String.format("\t;\tBASES %s", bases);
s += "\n";
s += ";\n";
// add bases and quals.
// add quals.
return s;
}