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Fixed docs for method and fixed the edge case optimization to properly use equals() on Integers. 

Shouldn't affect actual results at all.
This commit is contained in:
Eric Banks 2014-03-20 15:55:09 -04:00
parent 7117bebb5e
commit 0d82a70633
1 changed files with 4 additions and 4 deletions
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8
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
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@ -209,11 +209,11 @@ public final class FragmentUtils {
}
/**
* Merge two overlapping reads from the same fragment into a single super read, if possible
* Fix two overlapping reads from the same fragment by adjusting base qualities, if possible
*
* firstRead and secondRead must be part of the same fragment (though this isn't checked). Looks
* at the bases and alignment, and tries its best to create a meaningful synthetic single super read
* that represents the entire sequenced fragment.
* at the bases and alignment, and tries its best to create adjusted base qualities so that the observations
* are not treated independently.
*
* Assumes that firstRead starts before secondRead (according to their soft clipped starts)
*
@ -228,7 +228,7 @@ public final class FragmentUtils {
if ( ! clippedFirstRead.getReadName().equals(clippedSecondRead.getReadName()) ) throw new IllegalArgumentException("attempting to merge two reads with different names " + clippedFirstRead + " and " + clippedSecondRead);
// don't adjust fragments that do not overlap
if ( clippedFirstRead.getAlignmentEnd() < clippedSecondRead.getAlignmentStart() || clippedFirstRead.getReferenceIndex() != clippedSecondRead.getReferenceIndex() )
if ( clippedFirstRead.getAlignmentEnd() < clippedSecondRead.getAlignmentStart() || !clippedFirstRead.getReferenceIndex().equals(clippedSecondRead.getReferenceIndex()) )
return;
final Pair<Integer, Boolean> pair = ReadUtils.getReadCoordinateForReferenceCoordinate(clippedFirstRead, clippedSecondRead.getAlignmentStart());