Java Code Examples for htsjdk.samtools.QueryInterval#optimizeIntervals()

The following examples show how to use htsjdk.samtools.QueryInterval#optimizeIntervals() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: BAMInputFormat.java    From Hadoop-BAM with MIT License 6 votes vote down vote up 
/**
 * Converts a List of SimpleIntervals into the format required by the SamReader query API
 * @param rawIntervals SimpleIntervals to be converted
 * @return A sorted, merged list of QueryIntervals suitable for passing to the SamReader query API
 */
static QueryInterval[] prepareQueryIntervals( final List<Interval>
		rawIntervals, final SAMSequenceDictionary sequenceDictionary ) {
	if ( rawIntervals == null || rawIntervals.isEmpty() ) {
		return null;
	}

	// Convert each SimpleInterval to a QueryInterval
	final QueryInterval[] convertedIntervals =
			rawIntervals.stream()
					.map(rawInterval -> convertSimpleIntervalToQueryInterval(rawInterval, sequenceDictionary))
					.toArray(QueryInterval[]::new);

	// Intervals must be optimized (sorted and merged) in order to use the htsjdk query API
	return QueryInterval.optimizeIntervals(convertedIntervals);
}
Example 2
Source File: SamReaderQueryingIterator.java    From gatk with BSD 3-Clause "New" or "Revised" License 6 votes vote down vote up 
/**
 * Converts a List of SimpleIntervals into the format required by the SamReader query API
 * @param rawIntervals SimpleIntervals to be converted
 * @return A sorted, merged list of QueryIntervals suitable for passing to the SamReader query API
 */
private QueryInterval[] prepareQueryIntervals( final List<SimpleInterval> rawIntervals ) {
    if ( rawIntervals == null || rawIntervals.isEmpty() ) {
        return null;
    }

    // This might take a while with large interval lists, so log a status message
    logger.debug("Preparing intervals for traversal");

    // Convert each SimpleInterval to a QueryInterval
    final QueryInterval[] convertedIntervals =
            rawIntervals.stream()
            .map(rawInterval -> IntervalUtils.convertSimpleIntervalToQueryInterval(rawInterval, reader.getFileHeader().getSequenceDictionary()))
            .toArray(QueryInterval[]::new);

    // Intervals must be optimized (sorted and merged) in order to use the htsjdk query API
    return QueryInterval.optimizeIntervals(convertedIntervals);
}
Example 3
Source File: BamSlicerApplication.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up 
@NotNull
private static QueryInterval[] getIntervalsFromBED(@NotNull String bedPath, @NotNull SAMFileHeader header) throws IOException {
    Slicer bedSlicer = SlicerFactory.fromBedFile(bedPath);
    List<QueryInterval> queryIntervals = Lists.newArrayList();
    for (GenomeRegion region : bedSlicer.regions()) {
        queryIntervals.add(new QueryInterval(header.getSequenceIndex(region.chromosome()), (int) region.start(), (int) region.end()));
    }
    return QueryInterval.optimizeIntervals(queryIntervals.toArray(new QueryInterval[queryIntervals.size()]));
}
Example 4
Source File: SAMSlicer.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up 
@NotNull
private static QueryInterval[] createIntervals(@NotNull final Collection<GenomeRegion> regions, @NotNull final SAMFileHeader header) {
    final List<QueryInterval> queryIntervals = Lists.newArrayList();
    for (final GenomeRegion region : regions) {
        int sequenceIndex = header.getSequenceIndex(region.chromosome());
        if (sequenceIndex > -1) {
            queryIntervals.add(new QueryInterval(sequenceIndex, (int) region.start(), (int) region.end()));
        }
    }
    return QueryInterval.optimizeIntervals(queryIntervals.toArray(new QueryInterval[queryIntervals.size()]));
}
Example 5
Source File: SamSlicer.java    From hmftools with GNU General Public License v3.0 5 votes vote down vote up 
@NotNull
private static QueryInterval[] createIntervals(@NotNull final Collection<GenomeRegion> regions, @NotNull final SAMFileHeader header) {
    final List<QueryInterval> queryIntervals = Lists.newArrayList();
    for (final GenomeRegion region : regions) {
        int sequenceIndex = header.getSequenceIndex(region.chromosome());
        if (sequenceIndex > -1) {
            queryIntervals.add(new QueryInterval(sequenceIndex, (int) region.start(), (int) region.end()));
        }
    }
    return QueryInterval.optimizeIntervals(queryIntervals.toArray(new QueryInterval[queryIntervals.size()]));
}