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added MAF-style output 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1163 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-07-03 15:10:19 +00:00
parent dcb8892568
commit 25c30b12bb
1 changed files with 33 additions and 16 deletions
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49
java/src/org/broadinstitute/sting/playground/gatk/walkers/cancer/SomaticMutationWalker.java
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@ -50,6 +50,9 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
// @Argument(fullName = "output_failures", required = false, doc="produce output for failed sites")
public boolean OUTPUT_FAILURES = true;
@Argument(fullName = "output_format", shortName = "s3", required = true, doc="Format of output: bed or maf")
public String OUTPUT_FORMAT;
public void initialize() {
}
@ -260,23 +263,37 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
// if we're still here... we've got a somatic mutation! Output the results
// and stop looking for mutants!
String msg =
(failedMidpointCheck?"__FAILED-MPCHECK":"") +
"TScore:" + tumorLod +
"__TRefSum: " + tumorReadPile.qualitySums.getQualitySum(upRef) +
"__TAltSum: " + tumorReadPile.qualitySums.getQualitySum(altAllele) +
"__NScore:" + normalLod +
"__NRefSum: " + normalReadPile.qualitySums.getQualitySum(upRef) +
"__NAltSum: " + normalReadPile.qualitySums.getQualitySum(altAllele) +
"__maxSkewLod_" + failureReason.second + "_" +
"__MIDP: " + midp.get(altAllele);
if ("maf".equalsIgnoreCase(OUTPUT_FORMAT)) {
out.println(
"36\t" + //build
context.getContig() + "\t" +
context.getPosition() + "\t" +
context.getPosition() + "\t" +
upRef + "\t" +
upRef + "\t" +
altAllele + "\t" +
tumorSampleName + "\t" +
normalSampleName);
} else {
out.println(
context.getContig() + "\t" +
context.getPosition() + "\t" +
context.getPosition() + "\t"
+ msg.replace(' ','_')
);
String msg =
(failedMidpointCheck?"__FAILED-MPCHECK":"") +
"TScore:" + tumorLod +
"__TRefSum: " + tumorReadPile.qualitySums.getQualitySum(upRef) +
"__TAltSum: " + tumorReadPile.qualitySums.getQualitySum(altAllele) +
"__NScore:" + normalLod +
"__NRefSum: " + normalReadPile.qualitySums.getQualitySum(upRef) +
"__NAltSum: " + normalReadPile.qualitySums.getQualitySum(altAllele) +
"__maxSkewLod_" + failureReason.second + "_" +
"__MIDP: " + midp.get(altAllele);
out.println(
context.getContig() + "\t" +
context.getPosition() + "\t" +
context.getPosition() + "\t"
+ msg.replace(' ','_')
);
}