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Don't output callability metrics by default anymore; one can still have them output to the 'metrics' file (which is now @Hidden because they are really for GSA use). Added a TODO to move UG from @By reference to reads and rods once LIBS is cleaned up.

This commit is contained in:
Eric Banks 2012-04-19 11:45:56 -04:00
parent d3c84e7b1f
commit 76a6e37f4f
1 changed files with 3 additions and 8 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -116,6 +116,8 @@ import java.util.*;
@ReadFilters( {BadMateFilter.class, MappingQualityUnavailableFilter.class} ) @ReadFilters( {BadMateFilter.class, MappingQualityUnavailableFilter.class} )
@Reference(window=@Window(start=-200,stop=200)) @Reference(window=@Window(start=-200,stop=200))
@By(DataSource.REFERENCE) @By(DataSource.REFERENCE)
// TODO -- When LocusIteratorByState gets cleaned up, we should enable multiple @By sources:
// TODO -- @By( {DataSource.READS, DataSource.REFERENCE_ORDERED_DATA} )
@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250) @Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics>, AnnotatorCompatibleWalker { public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, UnifiedGenotyper.UGStatistics> implements TreeReducible<UnifiedGenotyper.UGStatistics>, AnnotatorCompatibleWalker {
@ -155,6 +157,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
@Argument(fullName = "debug_file", shortName = "debug_file", doc = "File to print all of the annotated and detailed debugging output", required = false) @Argument(fullName = "debug_file", shortName = "debug_file", doc = "File to print all of the annotated and detailed debugging output", required = false)
protected PrintStream verboseWriter = null; protected PrintStream verboseWriter = null;
@Hidden
@Argument(fullName = "metrics_file", shortName = "metrics", doc = "File to print any relevant callability metrics output", required = false) @Argument(fullName = "metrics_file", shortName = "metrics", doc = "File to print any relevant callability metrics output", required = false)
protected PrintStream metricsWriter = null; protected PrintStream metricsWriter = null;
@ -347,14 +350,6 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
} }
public void onTraversalDone(UGStatistics sum) { public void onTraversalDone(UGStatistics sum) {
logger.info(String.format("Visited bases %d", sum.nBasesVisited));
logger.info(String.format("Callable bases %d", sum.nBasesCallable));
logger.info(String.format("Confidently called bases %d", sum.nBasesCalledConfidently));
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 ) { if ( metricsWriter != null ) {
metricsWriter.println(String.format("Visited bases %d", sum.nBasesVisited)); metricsWriter.println(String.format("Visited bases %d", sum.nBasesVisited));
metricsWriter.println(String.format("Callable bases %d", sum.nBasesCallable)); metricsWriter.println(String.format("Callable bases %d", sum.nBasesCallable));