Package htsjdk.samtools.filter

Examples of htsjdk.samtools.filter.AggregateFilter

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        int fileIndex = 0;
        initializeNextBfqFiles(fileIndex++);

        int records = 0;

        final FilteringIterator it = new FilteringIterator(iterator, new AggregateFilter(filters));
        while (it.hasNext()) {
            final SAMRecord record = it.next();
            records++;
            if (records % increment == 0) {
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            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++;
            }
        }
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Related Classes of htsjdk.samtools.filter.AggregateFilter

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