Searched refs:queryIntervals (Results 1 – 5 of 5) sorted by relevance
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/iterators/ |
| H A D | SamReaderQueryingIterator.java | 36 private final QueryInterval[] queryIntervals; field in SamReaderQueryingIterator
60 …QueryingIterator( final SamReader reader, final List<SimpleInterval> queryIntervals, final boolean… in SamReaderQueryingIterator() argument
64 this.queryIntervals = prepareQueryIntervals(queryIntervals); in SamReaderQueryingIterator()
130 return reader.queryOverlapping(queryIntervals); in loadNextIterator()
141 return queryIntervals != null && queryIntervals.length > 0; in hasQueryIntervals()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/engine/ |
| H A D | ReadsPathDataSource.java | 388 …vate Iterator<GATKRead> prepareIteratorsForTraversal( final List<SimpleInterval> queryIntervals ) { in prepareIteratorsForTraversal() argument
389 return prepareIteratorsForTraversal(queryIntervals, false); in prepareIteratorsForTraversal()
398 …r<GATKRead> prepareIteratorsForTraversal( final List<SimpleInterval> queryIntervals, final boolean… in prepareIteratorsForTraversal() argument
403 …final boolean traversalIsBounded = (queryIntervals != null && ! queryIntervals.isEmpty()) || query… in prepareIteratorsForTraversal()
412 … getIntervalsOverlappingReader(readerEntry.getKey(), queryIntervals) : in prepareIteratorsForTraversal()
413 queryIntervals, in prepareIteratorsForTraversal()
440 final List<SimpleInterval> queryIntervals ) in getIntervalsOverlappingReader() argument
443 return queryIntervals.stream() in getIntervalsOverlappingReader()
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| /dports/biology/pbbam/pbbam-0.18.0/src/ |
| H A D | PbiFilterTypes.cpp | 200 const auto& queryIntervals = zmwFound->second; in Accepts() local
204 return queryIntervals.find(queryInterval) != queryIntervals.end(); in Accepts()
292 auto& queryIntervals = zmwPtr->at(zmw); in UpdateZmwQueryIntervals() local
293 queryIntervals.emplace(std::make_pair(queryStart, queryEnd)); in UpdateZmwQueryIntervals()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/iterators/ |
| H A D | SamReaderQueryingIteratorUnitTest.java | 72 …derQueryingIterator( final File inputBam, final List<SimpleInterval> queryIntervals, final boolean… in testSamReaderQueryingIterator() argument
74 …mReaderQueryingIterator iter = new SamReaderQueryingIterator(reader, queryIntervals, queryUnmapped… in testSamReaderQueryingIterator()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/ |
| H A D | ReadsPathDataSourceUnitTest.java | 456 …salWithUnmappedReads( final Path samFile, final List<SimpleInterval> queryIntervals, final boolean… in testTraversalWithUnmappedReads() argument
458 readsSource.setTraversalBounds(queryIntervals, queryUnmapped); in testTraversalWithUnmappedReads()
460 if ( (queryIntervals != null && ! queryIntervals.isEmpty()) || queryUnmapped ) { in testTraversalWithUnmappedReads()
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