Package org.broad.igv.sam

Examples of org.broad.igv.sam.Alignment

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        int nPairs = 0;

        while (alignments.hasNext()) {


            Alignment al = alignments.next();

            if (isProperPair(al)) {
                insertSizes[nPairs] = Math.abs(al.getInferredInsertSize());
                nPairs++;
            }


            if (nPairs >= MAX_PAIRS) {
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Related Classes of org.broad.igv.sam.Alignment

  • org.broad.igv.cli_plugin.AlignmentIOTest
  • org.broad.igv.cli_plugin.PluginSource
  • org.broad.igv.goby.GobyAlignmentQueryReaderTest
  • org.broad.igv.sam.reader.AlignmentReaderFactoryTest
  • org.broad.igv.sam.reader.BAMHttpQueryReaderTest
  • org.broad.igv.sam.reader.CGIAlignmentReader
  • org.broad.igv.sam.reader.GeraldReader$GeraldIterator
  • org.broad.igv.sam.reader.MergedAlignmentReader$MergedFileIterator
  • org.broad.igv.sam.reader.MergedAlignmentReader$MergedFileIterator$AlignmentStartComparator
  • org.broad.igv.sam.reader.MergedAlignmentReader$MergedFileIterator$RecordIterWrapper
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