Package htsjdk.samtools.filter

Examples of htsjdk.samtools.filter.WholeReadClippedFilter


        final Iterator<SAMRecord> iterator = (new SAMFileReader(IOUtil.openFileForReading(this.bamFile))).iterator();

        // Filter out noise reads and reads that fail the quality filter
        final TagFilter tagFilter = new TagFilter(ReservedTagConstants.XN, 1);
        final FailsVendorReadQualityFilter qualityFilter = new FailsVendorReadQualityFilter();
        final WholeReadClippedFilter clippedFilter = new WholeReadClippedFilter();


        if (!pairedReads) {
            List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
            filters.add(tagFilter);
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Related Classes of htsjdk.samtools.filter.WholeReadClippedFilter

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