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Fixed a bug wherein the loop variable for the second end of the pair was actually looping over the entire raw read (first and second ends combined). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@178 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-03-24 21:59:25 +00:00
parent c047b53d6b
commit 28c1330b4b
1 changed files with 6 additions and 6 deletions
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12
java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseRecaller.java
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@ -51,7 +51,7 @@ public class FourBaseRecaller {
FourIntensity[] intensities = ffp1.next().getIntensities(); FourIntensity[] intensities = ffp1.next().getIntensities();
String rsq = (CYCLE_START == 0) ? bfp1.next().getFirstReadSequence() : bfp1.next().getSecondReadSequence(); String rsq = (CYCLE_START == 0) ? bfp1.next().getFirstReadSequence() : bfp1.next().getSecondReadSequence();
for (int cycle = 0; cycle < intensities.length; cycle++) { for (int cycle = 0; cycle < readLength; cycle++) {
FourIntensity sig = intensities[cycle]; FourIntensity sig = intensities[cycle];
if (rsq.charAt(cycle) == 'A') { cmeans[cycle].add(Nucleotide.A, sig); } if (rsq.charAt(cycle) == 'A') { cmeans[cycle].add(Nucleotide.A, sig); }
@ -73,7 +73,7 @@ public class FourBaseRecaller {
FourIntensity[] intensities = ffp2.next().getIntensities(); FourIntensity[] intensities = ffp2.next().getIntensities();
String rsq = (CYCLE_START == 0) ? bfp2.next().getFirstReadSequence() : bfp2.next().getSecondReadSequence(); String rsq = (CYCLE_START == 0) ? bfp2.next().getFirstReadSequence() : bfp2.next().getSecondReadSequence();
for (int cycle = 0; cycle < intensities.length; cycle++) { for (int cycle = 0; cycle < readLength; cycle++) {
FourIntensity sig = intensities[cycle]; FourIntensity sig = intensities[cycle];
NucleotideChannelMeans mus = cmeans[cycle]; NucleotideChannelMeans mus = cmeans[cycle];
@ -103,11 +103,11 @@ public class FourBaseRecaller {
FourIntensity[] intensities = ffp3.next().getIntensities(); FourIntensity[] intensities = ffp3.next().getIntensities();
byte[] asciiseq = new byte[intensities.length]; byte[] asciiseq = new byte[readLength];
byte[] bestqual = new byte[intensities.length]; byte[] bestqual = new byte[readLength];
byte[] nextbestqual = new byte[intensities.length]; byte[] nextbestqual = new byte[readLength];
for (int cycle = 0; cycle < intensities.length; cycle++) { for (int cycle = 0; cycle < readLength; cycle++) {
FourIntensity fi = intensities[cycle]; FourIntensity fi = intensities[cycle];
double[] likes = new double[4]; double[] likes = new double[4];