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For Sendu: optionally emit a metrics file with callability info (including number of actual calls made) from UG 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3667 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-29 12:57:28 +00:00
parent 929e5b9276
commit ddf87e61c2
1 changed files with 21 additions and 1 deletions
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22
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -57,6 +57,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
@Argument(fullName = "verbose_mode", shortName = "verbose", doc = "File to print all of the annotated and detailed debugging output", required = false)
public PrintStream verboseWriter = null;
@Argument(fullName = "metrics_file", shortName = "metrics", doc = "File to print any relevant callability metrics output", required = false)
public PrintStream metricsWriter = null;
@Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
protected String[] annotationsToUse = {};
@ -88,6 +91,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
/** The number of bases called confidently (according to user threshold), either ref or other */
long nBasesCalledConfidently = 0;
/** The number of bases for which calls were emitted */
long nCallsMade = 0;
/** The total number of extended events encountered */
long nExtendedEvents = 0;
@ -178,6 +184,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
lhs.nBasesCallable += rhs.nBasesCallable;
lhs.nBasesCalledConfidently += rhs.nBasesCalledConfidently;
lhs.nBasesVisited += rhs.nBasesVisited;
lhs.nCallsMade += rhs.nCallsMade;
return lhs;
}
@ -192,7 +199,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
// A call was attempted -- the base was potentially callable
sum.nBasesCallable++;
// if the base was confidently called something, print it out
// the base was confidently callable
sum.nBasesCalledConfidently += value.confidentlyCalled ? 1 : 0;
// can't make a confident variant call here
@ -200,6 +207,8 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
return sum;
try {
// we are actually making a call
sum.nCallsMade++;
writer.addCall(value.vc, value.refAllele);
} catch (IllegalArgumentException e) {
throw new IllegalArgumentException(e.getMessage() + "; this is often caused by using the --assume_single_sample_reads argument with the wrong sample name");
@ -215,5 +224,16 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
logger.info(String.format("%% callable bases of all loci %3.3f", sum.percentCallableOfAll()));
logger.info(String.format("%% confidently called bases of all loci %3.3f", sum.percentCalledOfAll()));
logger.info(String.format("%% confidently called bases of callable loci %3.3f", sum.percentCalledOfCallable()));
logger.info(String.format("Actual calls made %d", sum.nCallsMade));
if ( metricsWriter != null ) {
metricsWriter.println(String.format("Visited bases %d", sum.nBasesVisited));
metricsWriter.println(String.format("Callable bases %d", sum.nBasesCallable));
metricsWriter.println(String.format("Confidently called bases %d", sum.nBasesCalledConfidently));
metricsWriter.println(String.format("%% callable bases of all loci %3.3f", sum.percentCallableOfAll()));
metricsWriter.println(String.format("%% confidently called bases of all loci %3.3f", sum.percentCalledOfAll()));
metricsWriter.println(String.format("%% confidently called bases of callable loci %3.3f", sum.percentCalledOfCallable()));
metricsWriter.println(String.format("Actual calls made %d", sum.nCallsMade));
}
}
}