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more verbose gff output! 

EVEN MORE verbosity to come! 

Tremble in anticipation.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@382 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-04-13 15:21:23 +00:00
parent cf929a8275
commit 6652f13a17
1 changed files with 15 additions and 5 deletions
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20
java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
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@ -61,14 +61,24 @@ public class AlleleFrequencyEstimate {
public String asGFFString() public String asGFFString()
{ {
return String.format("%s\tCALLER\tVARIANT\t%s\t%s\t%f\t.\t.\tREF %c\t;\tALT %c\t;\tFREQ %f\n", String s = "";
s += String.format("%s\tCALLER\tVARIANT\t%s\t%s\t%f\t.\t.\t",
location.getContig(), location.getContig(),
location.getStart(), location.getStart(),
location.getStart(), location.getStart(),
lodVsRef, lodVsRef);
ref, s += String.format("REF %c\t;\t", ref);
alt, s += String.format("ALT %c\t;\t", alt);
qhat); 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 += "\n";
// add bases and quals.
return s;
} }
public String asTabularString() { public String asTabularString() {