Package org.broadinstitute.gatk.engine.alignment

Examples of org.broadinstitute.gatk.engine.alignment.Alignment


                //throw new GATKException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count));
                System.out.printf("Unable to align read %s to reference; count = %d%n",read.getReadName(),count);
                failures++;
            }

            Alignment foundAlignment = null;
            for(Alignment[] alignmentsOfQuality: alignments) {
                for(Alignment alignment: alignmentsOfQuality) {
                    if( read.getReadNegativeStrandFlag() != alignment.isNegativeStrand() )
                        continue;
                    if( read.getAlignmentStart() != alignment.getAlignmentStart() )
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Related Classes of org.broadinstitute.gatk.engine.alignment.Alignment

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