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

Cleanup from previous commit

This commit is contained in:
Eric Banks 2012-07-03 14:42:44 -04:00
parent 0b37d44b0d
commit 344c3aeb1d
2 changed files with 3 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java
View File

@ -85,7 +85,7 @@ public class Datum {
double empiricalQualDouble() { double empiricalQualDouble() {
final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT); final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT);
final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT); final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT);
double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations); final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations);
return Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE); return Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE);
} }

3
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java
View File

@ -57,7 +57,8 @@ public class RecalDatum extends Datum {
public RecalDatum(final long _numObservations, final long _numMismatches, final byte reportedQuality) { public RecalDatum(final long _numObservations, final long _numMismatches, final byte reportedQuality) {
numObservations = _numObservations; numObservations = _numObservations;
numMismatches = _numMismatches; numMismatches = _numMismatches;
estimatedQReported = QualityUtils.qualToErrorProb(reportedQuality); estimatedQReported = reportedQuality;
empiricalQuality = UNINITIALIZED;
} }
public RecalDatum(final RecalDatum copy) { public RecalDatum(final RecalDatum copy) {