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Fixed a bug in the parsing of the second end of the pair. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@168 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-03-24 14:34:37 +00:00
parent 786a7845dd
commit 88d94d407a
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java
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@ -99,7 +99,8 @@ public class FirecrestFileParser extends AbstractFirecrestFileParser {
intensities[cycle] = new FourIntensity(fIntensities);
}
FourIntensity[] intensities2 = new FourIntensity[(cycle_start > 0 && cycle_stop > 0 && cycle_stop > cycle_start) ? numIntensities : (cycle_stop - cycle_start)];
FourIntensity[] intensities2 = new FourIntensity[(cycle_start > 0 && cycle_stop > 0 && cycle_stop > cycle_start) ? (cycle_stop - cycle_start) : numIntensities];
for (int cycle = 0, offset = (cycle_start >= 0 ? cycle_start : 0); cycle < intensities2.length; cycle++) {
intensities2[cycle] = intensities[offset + cycle];
}