Examples of htsjdk.samtools.filter.FailsVendorReadQualityFilter


        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>();

        if (!this.pairedReads) {
            // Filter out noise reads and reads that fail the quality filter
            final List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
            filters.add(new TagFilter(ReservedTagConstants.XN, 1));
            if (!this.includeNonPfReads) {
                filters.add(new FailsVendorReadQualityFilter());
            }
            final FilteringIterator itr = new FilteringIterator(it, new AggregateFilter(filters));
            while (itr.hasNext()) {
                itr.next();
                count++;

Related Classes of htsjdk.samtools.filter.FailsVendorReadQualityFilter

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