Java Code Examples for htsjdk.samtools.SAMFileHeader#getSequenceIndex()
The following examples show how to use
htsjdk.samtools.SAMFileHeader#getSequenceIndex() .
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Example 1
Source File: BamSlicer.java From hmftools with GNU General Public License v3.0 | 6 votes |
private static QueryInterval[] createIntervals(@NotNull final List<GenomeRegion> regions, @NotNull final SAMFileHeader header) { final QueryInterval[] queryIntervals = new QueryInterval[regions.size()]; for (int i = 0; i < regions.size(); ++i) { final GenomeRegion region = regions.get(i); int sequenceIndex = header.getSequenceIndex(region.chromosome()); if (sequenceIndex < 0) return null; queryIntervals[i] = new QueryInterval(sequenceIndex, (int) region.start(), (int) region.end()); } return queryIntervals; }
Example 2
Source File: SAMSlicer.java From hmftools with GNU General Public License v3.0 | 5 votes |
@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 3
Source File: SamSlicer.java From hmftools with GNU General Public License v3.0 | 5 votes |
@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 4
Source File: BAMQueryFilteringIterator.java From cramtools with Apache License 2.0 | 5 votes |
public BAMQueryFilteringIterator(final CloseableIterator<SAMRecord> iterator, final String sequence, final int start, final int end, final QueryType queryType, SAMFileHeader fileHeader) { this.wrappedIterator = iterator; mReferenceIndex = fileHeader.getSequenceIndex(sequence); mRegionStart = start; if (queryType == QueryType.STARTING_AT) { mRegionEnd = mRegionStart; } else { mRegionEnd = (end <= 0) ? Integer.MAX_VALUE : end; } mQueryType = queryType; mNextRecord = advance(); }