c98df0a8627db70e9806bb7534c344d402155f5d,java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java,CovariateCounterWalker,map,#RefMetaDataTracker#ReferenceContext#AlignmentContext#,229

Before Change


                    if( BaseUtils.isRegularBase( (char)(bases[offset]) ) ) {

                        // SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it
                        if( !read.getReadGroup().getPlatform().equalsIgnoreCase("SOLID") || RAC.SOLID_RECAL_MODE.equalsIgnoreCase("DO_NOTHING") || !RecalDataManager.isInconsistentColorSpace( read, offset ) ) {

                            // This base finally passed all the checks for a good base, so add it to the big data hashmap
                            updateDataFromRead( read, offset, refBase );

After Change


                    if( BaseUtils.isRegularBase( (char)(bases[offset]) ) ) {

                        // SOLID bams have inserted the reference base into the read if the color space in inconsistent with the read base so skip it
                        if( !read.getReadGroup().getPlatform().toUpperCase().contains("SOLID") || RAC.SOLID_RECAL_MODE.equalsIgnoreCase("DO_NOTHING") || !RecalDataManager.isInconsistentColorSpace( read, offset ) ) {

                            // This base finally passed all the checks for a good base, so add it to the big data hashmap
                            updateDataFromRead( read, offset, refBase );