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For Sendu: a similar addition to the Indel Genotyper allowing it to emit a metrics file (which for now consists only of # of normal/tumor calls made) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3668 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-29 13:19:17 +00:00
parent ddf87e61c2
commit 801b47c6e9
1 changed files with 14 additions and 0 deletions
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14
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -55,6 +55,7 @@ import org.broadinstitute.sting.commandline.Argument;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.io.PrintStream;
import java.util.*; import java.util.*;
/** /**
@ -71,6 +72,10 @@ import java.util.*;
public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> { public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
@Argument(fullName="outputFile", shortName="O", doc="output file name (defaults to BED format)", required=true) @Argument(fullName="outputFile", shortName="O", doc="output file name (defaults to BED format)", required=true)
java.io.File bed_file; java.io.File bed_file;
@Argument(fullName = "metrics_file", shortName = "metrics", doc = "File to print callability metrics output", required = false)
public PrintStream metricsWriter = null;
@Argument(fullName="1kg_format", shortName="1kg", doc="output in 1000 genomes format", required=false) @Argument(fullName="1kg_format", shortName="1kg", doc="output in 1000 genomes format", required=false)
boolean FORMAT_1KG = false; boolean FORMAT_1KG = false;
@Argument(fullName="somatic", shortName="somatic", @Argument(fullName="somatic", shortName="somatic",
@ -118,6 +123,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
private String refName = null; private String refName = null;
private java.io.Writer output = null; private java.io.Writer output = null;
private GenomeLoc location = null; private GenomeLoc location = null;
private long normalCallsMade = 0L, tumorCallsMade = 0L;
boolean outOfContigUserWarned = false; boolean outOfContigUserWarned = false;
@ -410,6 +416,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
} }
if ( normalCall.isCall() ) { if ( normalCall.isCall() ) {
normalCallsMade++;
String message = normalCall.makeBedLine(output); String message = normalCall.makeBedLine(output);
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList)); String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
@ -581,6 +588,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
} }
if ( tumorCall.isCall() ) { if ( tumorCall.isCall() ) {
tumorCallsMade++;
String message = tumorCall.makeBedLine(output); String message = tumorCall.makeBedLine(output);
String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList)); String annotationString = (refseqIterator == null ? "" : getAnnotationString(annotationList));
@ -660,6 +668,12 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
public void onTraversalDone(Integer result) { public void onTraversalDone(Integer result) {
if ( call_somatic ) emit_somatic(1000000000, true); if ( call_somatic ) emit_somatic(1000000000, true);
else emit(1000000000,true); // emit everything we might have left else emit(1000000000,true); // emit everything we might have left
if ( metricsWriter != null ) {
metricsWriter.println(String.format("Normal calls made %d", normalCallsMade));
metricsWriter.println(String.format("Tumor calls made %d", tumorCallsMade));
}
try { try {
output.close(); output.close();
} catch (IOException e) { } catch (IOException e) {