Examples with IntervalFilter htsjdk.samtools.filter.IntervalFilter used on opensource projects

Example 1 with IntervalFilter

use of htsjdk.samtools.filter.IntervalFilter in project jvarkit by lindenb.

the class MultiBamLauncher method openSamIterator.

/**
 * create input SAMRecord iterator for one sample
 */
protected CloseableIterator<SAMRecord> openSamIterator(final SamReader sr) {
    if (this.regionFiles != null) {
        this.regionFiles.dictionary(SequenceDictionaryUtils.extractRequired(sr.getFileHeader()));
        if (!sr.hasIndex()) {
            final List<Interval> L = this.regionFiles.stream().map(x -> new Interval(x)).collect(Collectors.toList());
            final SAMRecordIterator st0 = sr.iterator();
            return new FilteringSamIterator(st0, new IntervalFilter(L, sr.getFileHeader()));
        } else {
            final QueryInterval[] optimized = this.regionFiles.optimizedQueryIntervals();
            return sr.query(optimized, false);
        }
    }
    return sr.iterator();
}

Example 2 with IntervalFilter

use of htsjdk.samtools.filter.IntervalFilter in project jvarkit by lindenb.

the class SamReadLengthDistribution method openSamIterator.

/**
 * create input SAMRecord iterator
 */
private CloseableIterator<SAMRecord> openSamIterator(final SamReader sr) {
    if (this.regionFiles != null) {
        this.regionFiles.dictionary(SequenceDictionaryUtils.extractRequired(sr.getFileHeader()));
        if (!sr.hasIndex()) {
            final List<Interval> L = this.regionFiles.stream().map(x -> new Interval(x)).collect(Collectors.toList());
            final SAMRecordIterator st0 = sr.iterator();
            return new FilteringSamIterator(st0, new IntervalFilter(L, sr.getFileHeader()));
        } else {
            return sr.query(this.regionFiles.optimizedQueryIntervals(), false);
        }
    }
    return sr.iterator();
}