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fixing insidious bugs 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@879 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-06-02 18:33:45 +00:00
parent 6e60cddfed
commit 7e7c83ddca
2 changed files with 3 additions and 3 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java
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@ -17,7 +17,7 @@ public class LogisticRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWr
public String logisticParamsFile;
@Argument(shortName="outputBAM", doc="output BAM file", required=false)
public String outputBamFile = "";
public String outputBamFile = null;
HashMap<String, LogisticRegressor> regressors = new HashMap<String, LogisticRegressor>();
private static Logger logger = Logger.getLogger(LogisticRecalibrationWalker.class);
@ -120,7 +120,7 @@ public class LogisticRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWr
//newQual = QualityUtils.probToQual(P);
//newQual = (byte)Math.min(Math.round(-10*logPOver1minusP),63);
//System.out.printf("Recal %s %d %d => %f => %f leads to %d%n", dinuc, cycle, qual, logPOver1minusP, P, newQual);
//System.out.printf("Recal %s %d %d %d%n", dinuc, cycle, qual, newQual);
}else{
newQual = qual;
}

2
java/src/org/broadinstitute/sting/utils/BaseUtils.java
View File

@ -184,7 +184,7 @@ public class BaseUtils {
byte[] rcbases = new byte[bases.length];
for (int i = 0; i < bases.length; i++) {
rcbases[i] = bases[bases.length - 1];
rcbases[i] = bases[bases.length - i - 1];
}
return rcbases;