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making sure the output is as pretty as I said it would be on the wiki. 

wikipage for this walker is up, at : http://www.broadinstitute.org/gsa/wiki/index.php/Genotype_and_Validate#Examples

use it ;)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5442 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-03-14 20:32:09 +00:00
parent 239dae0985
commit fcc347bb05
1 changed files with 15 additions and 12 deletions
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27
java/src/org/broadinstitute/sting/playground/gatk/walkers/GenotypeAndValidateWalker.java
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@ -166,8 +166,10 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
return counter;
// Do not operate on variants that are not covered to the optional minimum depth
if (!context.hasReads() || minDepth > 0 && context.getBasePileup().getBases().length < minDepth) {
counter.numUncovered = 1L;
if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
// don't count indel extended events multiple times as uncovered.
// if (vcComp.getStart() == ref.getLocus().getStart()) //todo - not sure I want this, may be misleading to filter anything.
counter.numUncovered = 1L;
return counter;
}
@ -179,15 +181,15 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
call = snpEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
else if ( vcComp.isIndel() ) {
call = indelEngine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
if (call.vc == null) // variant context will be null on an extended indel event and I just want to call it one event.
return counter;
// if (call.vc == null) // variant context will be null on an extended indel event and I just want to call it one event.
// return counter;
}
else {
logger.info("Not SNP or INDEL " + vcComp.getChr() + ":" + vcComp.getStart() + " " + vcComp.getAlleles());
return counter;
}
if (!call.confidentlyCalled) {
if (!call.confidentlyCalled) { //todo - maybe filter extended indel events to count as one only if it's entirely successful?
counter.numNotConfidentCalls = 1L;
if (vcComp.getFilters().contains("TP"))
counter.numFN = 1L;
@ -227,14 +229,15 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
}
public void onTraversalDone( CountedData reduceSum ) {
logger.info("TP = " + reduceSum.numTP);
logger.info("TN = " + reduceSum.numTN);
logger.info("FP = " + reduceSum.numFP);
logger.info("FN = " + reduceSum.numFN);
logger.info("PPV = " + ((double) reduceSum.numTP /( reduceSum.numTP + reduceSum.numFP)));
logger.info("NPV = " + ((double) reduceSum.numTN /( reduceSum.numTN + reduceSum.numFN)));
logger.info("Uncovered = " + reduceSum.numUncovered);
logger.info("(status / truth)");
logger.info("called / true = " + reduceSum.numTP);
logger.info("not called / false = " + reduceSum.numTN);
logger.info("called /false = " + reduceSum.numFP);
logger.info("not called / true = " + reduceSum.numFN);
logger.info("PPV = " + 100 * ((double) reduceSum.numTP /( reduceSum.numTP + reduceSum.numFP)) + "%");
logger.info("NPV = " + 100 * ((double) reduceSum.numTN /( reduceSum.numTN + reduceSum.numFN)) + "%");
logger.info("confidently called = " + reduceSum.numConfidentCalls);
logger.info("not confidently called = " + reduceSum.numNotConfidentCalls );
logger.info("Uncovered = " + reduceSum.numUncovered);
}
}