Package htsjdk.samtools.filter

Examples of htsjdk.samtools.filter.SecondaryAlignmentFilter


        final CountingFilter mapqFilter       = new CountingMapQFilter(MINIMUM_MAPPING_QUALITY);
        final CountingPairedFilter pairFilter = new CountingPairedFilter();
        filters.add(mapqFilter);
        filters.add(dupeFilter);
        filters.add(pairFilter);
        filters.add(new SecondaryAlignmentFilter()); // Not a counting filter because we never want to count reads twice
        iterator.setSamFilters(filters);
        iterator.setEmitUncoveredLoci(true);
        iterator.setMappingQualityScoreCutoff(0); // Handled separately because we want to count bases
        iterator.setQualityScoreCutoff(0);        // Handled separately because we want to count bases
        iterator.setIncludeNonPfReads(false);
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Related Classes of htsjdk.samtools.filter.SecondaryAlignmentFilter

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