zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
View File

@ -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 * 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 * at the bases and alignment, and tries its best to create adjusted base qualities so that the observations
* that represents the entire sequenced fragment. * are not treated independently.
* *
* Assumes that firstRead starts before secondRead (according to their soft clipped starts) * 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); 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 // 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; return;
final Pair<Integer, Boolean> pair = ReadUtils.getReadCoordinateForReferenceCoordinate(clippedFirstRead, clippedSecondRead.getAlignmentStart()); final Pair<Integer, Boolean> pair = ReadUtils.getReadCoordinateForReferenceCoordinate(clippedFirstRead, clippedSecondRead.getAlignmentStart());