Examples of GATKSAMRecord

org.broadinstitute.gatk.utils.sam.GATKSAMRecord

@author ebanks, depristoGATKSAMRecord this class extends the samtools BAMRecord class (and SAMRecord) and caches important (and oft-accessed) data that's not already cached by the SAMRecord class IMPORTANT NOTE: Because ReadGroups are not set through the SAMRecord, if they are ever modified externally then one must also invoke the setReadGroup() method here to ensure that the cache is kept up-to-date. WARNING -- GATKSAMRecords cache several values (that are expensive to compute) that depending on the inferred insert size and alignment starts and stops of this read and its mate. Changing these values in any way will invalidate the cached value. However, we do not monitor those setter functions, so modifying a GATKSAMRecord in any way may result in stale cached values.

        }


        final int[] hapReadsNotInReference = new int[haplotypes.size()];


        for (int i = 0; i < readCount; i++) {
            final GATKSAMRecord r = as.readList().get(i);


            final int hapNumber = i % haplotypes.size();
            final int offset = i % (haplotypes.get(hapNumber).length() - readLength);
            Assert.assertEquals(r.getReadString(),haplotypes.get(hapNumber).getBaseString().substring(offset,offset+readLength));
            if (as.getReference().indexOf(r.getReadString()) == -1) {
                hapReadsNotInReference[hapNumber]++;
            }
        }


        Assert.assertEquals(hapReadsNotInReference[0],0);

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Examples of GATKSAMRecord

Examples of org.broadinstitute.gatk.utils.sam.GATKSAMRecord