zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Trivial change to verbose 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2203 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-01 20:48:10 +00:00
parent 74f6526e09
commit c36069355e
1 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/FourBaseProbabilities.java
View File

@ -154,7 +154,7 @@ public abstract class FourBaseProbabilities implements Cloneable {
log10Likelihoods[BaseUtils.simpleBaseToBaseIndex(base)] += likelihood; log10Likelihoods[BaseUtils.simpleBaseToBaseIndex(base)] += likelihood;
} }
if ( isVerbose() ) { if ( verbose ) {
for ( char base : BaseUtils.BASES ) { System.out.printf("%s\t", base); } for ( char base : BaseUtils.BASES ) { System.out.printf("%s\t", base); }
System.out.println(); System.out.println();
for ( char base : BaseUtils.BASES ) { System.out.printf("%.2f\t", log10Likelihoods[BaseUtils.simpleBaseToBaseIndex(base)]); } for ( char base : BaseUtils.BASES ) { System.out.printf("%.2f\t", log10Likelihoods[BaseUtils.simpleBaseToBaseIndex(base)]); }
@ -188,7 +188,7 @@ public abstract class FourBaseProbabilities implements Cloneable {
for ( char base : BaseUtils.BASES ) { for ( char base : BaseUtils.BASES ) {
double likelihood = log10PofObservingBaseGivenChromosome(observedBase, base, qualityScore, read, offset); double likelihood = log10PofObservingBaseGivenChromosome(observedBase, base, qualityScore, read, offset);
if ( isVerbose() ) { if ( verbose ) {
boolean fwdStrand = ! read.getReadNegativeStrandFlag(); boolean fwdStrand = ! read.getReadNegativeStrandFlag();
System.out.printf(" L(%c | b=%s, Q=%d, S=%s) = %f / %f%n", System.out.printf(" L(%c | b=%s, Q=%d, S=%s) = %f / %f%n",
observedBase, base, qualityScore, fwdStrand ? "+" : "-", pow(10,likelihood) * 100, likelihood); observedBase, base, qualityScore, fwdStrand ? "+" : "-", pow(10,likelihood) * 100, likelihood);