Package | Description |
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htsjdk.samtools | |
htsjdk.samtools.util |
Modifier and Type | Class and Description |
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class |
SAMFileReader
Deprecated.
|
class |
SAMFileTruncatedReader
Deprecated.
|
static class |
SamReader.PrimitiveSamReaderToSamReaderAdapter
Decorator for a
SamReader.PrimitiveSamReader that expands its functionality into a SamReader ,
given the backing SamInputResource . |
Modifier and Type | Method and Description |
---|---|
SamReader |
CRAMIterator.getFileSource() |
SamReader |
SAMFileSource.getReader()
Retrieves the reader from which this read was initially retrieved.
|
SamReader |
SAMRecordSetBuilder.getSamReader()
Creates samFileReader from the data in instance of this class
|
SamReader |
CustomReaderFactory.maybeOpen(java.net.URL url)
Check if the url is supposed to be handled by the custom factory and if so
attempt to create reader via an instance of this custom factory.
|
abstract SamReader |
SamReaderFactory.open(java.io.File file) |
abstract SamReader |
SamReaderFactory.open(SamInputResource resource) |
SamReader |
CustomReaderFactory.ICustomReaderFactory.open(java.net.URL url) |
Modifier and Type | Method and Description |
---|---|
java.util.Collection<SamReader> |
SamFileHeaderMerger.getReaders()
Deprecated.
replaced by getHeaders()
|
Modifier and Type | Method and Description |
---|---|
static void |
BAMIndexer.createIndex(SamReader reader,
java.io.File output)
Generates a BAM index file from an input BAM file
|
static void |
BAMIndexer.createIndex(SamReader reader,
java.io.File output,
Log log)
Generates a BAM index file from an input BAM file
|
static int |
BamIndexValidator.exhaustivelyTestIndex(SamReader reader) |
java.lang.Integer |
SamFileHeaderMerger.getMergedSequenceIndex(SamReader reader,
java.lang.Integer oldReferenceSequenceIndex)
Deprecated.
replaced by getMergedSequenceIndex(SAMFileHeader, Integer)
|
java.lang.String |
SamFileHeaderMerger.getProgramGroupId(SamReader reader,
java.lang.String originalProgramGroupId)
Deprecated.
replaced by getProgramGroupId(SAMFileHeader, String)
|
java.lang.String |
SamFileHeaderMerger.getReadGroupId(SamReader reader,
java.lang.String originalReadGroupId)
Deprecated.
replaced by getReadGroupId(SAMFileHeader, String)
|
static int |
BamIndexValidator.lessExhaustivelyTestIndex(SamReader reader)
A less time-consuming index validation that only looks at the first and last references in the index
and the first and last chunks in each of those
|
static DownsamplingIterator |
DownsamplingIteratorFactory.make(SamReader reader,
DownsamplingIteratorFactory.Strategy strategy,
double proportion,
double accuracy,
int seed)
Convenience method that constructs a downsampling iterator for all the reads available from a SamReader.
|
abstract void |
SamReaderFactory.reapplyOptions(SamReader reader)
Reapplies any changed options to the reader *
|
void |
CRAMIterator.setFileSource(SamReader mReader) |
boolean |
SamFileValidator.validateSamFileSummary(SamReader samReader,
ReferenceSequenceFile reference)
Outputs validation summary report to out.
|
boolean |
SamFileValidator.validateSamFileVerbose(SamReader samReader,
ReferenceSequenceFile reference)
Outputs validation error details to out.
|
Constructor and Description |
---|
SAMFileSource(SamReader reader,
SAMFileSpan filePointer)
Create a new SAMFileSource with the given reader and file pointer.
|
SAMLineParser(SAMFileHeader samFileHeader,
SamReader samFileReader,
java.io.File samFile)
Public constructor.
|
SAMLineParser(SAMRecordFactory samRecordFactory,
ValidationStringency validationStringency,
SAMFileHeader samFileHeader,
SamReader samFileReader,
java.io.File samFile)
Public constructor.
|
Constructor and Description |
---|
MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
java.util.Collection<SamReader> readers,
boolean assumeSorted)
Constructs a new merging iterator with the same set of readers and sort order as
provided by the header merger parameter.
|
MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
java.util.Map<SamReader,CloseableIterator<SAMRecord>> iterators,
boolean assumeSorted)
Add a set of SAM file iterators to the merging iterator.
|
SamFileHeaderMerger(java.util.Collection<SamReader> readers,
SAMFileHeader.SortOrder sortOrder)
Deprecated.
replaced by SamFileHeaderMerger(Collection
|
SamFileHeaderMerger(java.util.Collection<SamReader> readers,
SAMFileHeader.SortOrder sortOrder,
boolean mergeDictionaries)
Deprecated.
replaced by SamFileHeaderMerger(Collection
|
Modifier and Type | Method and Description |
---|---|
long |
QualityEncodingDetector.add(long maxRecords,
SamReader reader)
Adds the provided reader's records to the detector.
|
static FastqQualityFormat |
QualityEncodingDetector.detect(long maxRecords,
SamReader reader) |
static FastqQualityFormat |
QualityEncodingDetector.detect(SamReader reader) |
static FastqQualityFormat |
QualityEncodingDetector.detect(SamReader reader,
FastqQualityFormat expectedQualityFormat)
Reads through the records in the provided SAM reader and uses their quality scores to sanity check the expected
quality passed in.
|
CloseableIterator<SAMRecord> |
SamRecordIntervalIteratorFactory.makeSamRecordIntervalIterator(SamReader samReader,
java.util.List<Interval> uniqueIntervals,
boolean useIndex) |
Constructor and Description |
---|
SamLocusIterator(SamReader samReader)
Prepare to iterate through the given SAM records, skipping non-primary alignments.
|
SamLocusIterator(SamReader samReader,
IntervalList intervalList)
Prepare to iterate through the given SAM records, skipping non-primary alignments.
|
SamLocusIterator(SamReader samReader,
IntervalList intervalList,
boolean useIndex)
Prepare to iterate through the given SAM records, skipping non-primary alignments
|