Projects >> gatk >>764c8a5ec348e989eec12618bf4b765048a79a88

Chunk
Conflicting content 
                final GATKSAMRecord read = p.getRead();
                final int offset = p.getOffset();

<<<<<<< HEAD
                // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
                if (readHasBeenSkipped(read) || isLowQualityBase(read, offset))
=======
                if (readHasBeenSkipped(read) || isLowQualityBase(p))                                         // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
>>>>>>> 2d7797a4cf5256988631075f56658e09685e5dda
                    continue;

                if (readNotSeen(read)) {
Solution content 
                final GATKSAMRecord read = p.getRead();
                final int offset = p.getOffset();

                // This read has been marked to be skipped or base is low quality (we don't recalibrate low quality bases)
                if (readHasBeenSkipped(read) || isLowQualityBase(p))
                    continue;

                if (readNotSeen(read)) {
File
BaseRecalibrator.java
Developer's decision
Manual
Kind of conflict
Comment
If statement