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Saw that one of the offsets needed to be changed from - 1 to -2 and changed the wrong damn offset. Fixed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@915 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-05 19:18:34 +00:00
parent 4623a34ad3
commit 34bb43a6c8
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/LogisticRecalibrationWalker.java
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@ -34,12 +34,12 @@ public class LogisticRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWr
LogisticRegressor regressor = new LogisticRegressor(2, 4);
regressors.put(new Pair<String,String>(readGroup,dinuc), regressor);
System.out.printf("Vals = %s%n", Utils.join(",", vals));
for ( int i = 2; i <= (vals.length-2); i++ ) {
Pair<Integer, Integer> ij = mapping.get(i-1);
for ( int i = 2; i < vals.length; i++ ) {
Pair<Integer, Integer> ij = mapping.get(i-2);
try {
double c = Double.parseDouble(vals[i]);
regressor.setCoefficient(ij.first, ij.second, c);
System.out.printf("Setting coefficient %s,%s => %s = %f%n", readGroup, dinuc, ij, c);
System.out.printf("Setting coefficient %s,%s => %s = %1.12f%n", readGroup, dinuc, ij, c);
} catch ( NumberFormatException e ) {
Utils.scareUser("Badly formed logistic regression header at " + vals[i] + " line: " + line );
}