90a053ea935ea6868008bacc9b6d96cf8dd3644a,public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java,IndelRealigner,clean,#ReadBin#,658

Before Change


                        // For now, we will just arbitrarily add 10 to the mapping quality. [EB, 6/7/2010].
                        // TODO -- we need a better solution here
                        GATKSAMRecord read = aRead.getRead();
                        read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));

                        // before we fix the attribute tags we first need to make sure we have enough of the reference sequence
                        int neededBasesToLeft = leftmostIndex - read.getAlignmentStart();

After Change


                        // TODO -- we need a better solution here
                        GATKSAMRecord read = aRead.getRead();
                        if ( read.getMappingQuality() != 255 ) // 255 == Unknown, so don't modify it
                            read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));

                        // before we fix the attribute tags we first need to make sure we have enough of the reference sequence
                        int neededBasesToLeft = leftmostIndex - read.getAlignmentStart();