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Clarifying the comment regarding differentiating between first and second of pair in CycleCovariate. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2594 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2010-01-15 18:36:14 +00:00
parent b911b7df82
commit ba2acda406
1 changed files with 5 additions and 3 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
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@ -143,10 +143,12 @@ public class CycleCovariate implements StandardCovariate {
return getValue( read, offset ); // A recursive call
}
// Differentiate between first and second of pair
// Differentiate between first and second of pair.
// The sequencing machine cycle keeps incrementing for the second read in a pair. So it is possible for a read group
// to have an error affecting quality at a particular cycle on only second of pair reads. Therefore the cycle covariate must differentiate
// between first and second of pair reads.
// to have an error affecting quality at a particular cycle on the first of pair which carries over to the second of pair.
// Therefore the cycle covariate must differentiate between first and second of pair reads.
// This effect can not be corrected by pulling out the first of pair and second of pair flags into a separate covariate because
// the current sequential model would consider the effects independently instead of jointly.
if( read.getReadPairedFlag() && read.getSecondOfPairFlag() ) {
cycle *= -1;
}