Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.cram.build | |
htsjdk.samtools.cram.structure | |
htsjdk.samtools.filter | |
htsjdk.samtools.sra | |
htsjdk.samtools.util |
Modifier and Type | Method and Description |
---|---|
SAMFileHeader |
SAMFileHeader.clone() |
SAMFileHeader |
SAMTextHeaderCodec.decode(LineReader reader,
String source)
Reads text SAM header and converts to a SAMFileHeader object.
|
SAMFileHeader |
SamReader.getFileHeader() |
SAMFileHeader |
SamReader.PrimitiveSamReader.getFileHeader() |
SAMFileHeader |
SamReader.PrimitiveSamReaderToSamReaderAdapter.getFileHeader() |
SAMFileHeader |
SAMLineParser.getFileHeader()
Get the File header.
|
SAMFileHeader |
SAMFileReader.getFileHeader()
Deprecated.
|
SAMFileHeader |
SRAFileReader.getFileHeader() |
SAMFileHeader |
SAMFileWriterImpl.getFileHeader() |
SAMFileHeader |
CRAMFileReader.getFileHeader() |
SAMFileHeader |
SAMFileWriter.getFileHeader() |
abstract SAMFileHeader |
SamReaderFactory.getFileHeader(File samFile)
Utility method to open the file get the header and close the file
|
SAMFileHeader |
SAMRecordSetBuilder.getHeader() |
SAMFileHeader |
SAMRecord.getHeader() |
SAMFileHeader |
SamFileHeaderMerger.getMergedHeader()
Returns the merged header that should be written to any output merged file.
|
SAMFileHeader |
MergingSamRecordIterator.getMergedHeader()
Returns the merged header that the merging iterator is working from.
|
SAMFileHeader |
CRAMIterator.getSAMFileHeader() |
Modifier and Type | Method and Description |
---|---|
Collection<SAMFileHeader> |
SamFileHeaderMerger.getHeaders()
Returns the collection of readers that this header merger is working with.
|
Modifier and Type | Method and Description |
---|---|
static void |
SAMUtils.chainSAMProgramRecord(SAMFileHeader header,
SAMProgramRecord program)
Chains
program in front of the first "head" item in the list of
SAMProgramRecords in header . |
BAMRecord |
DefaultSAMRecordFactory.createBAMRecord(SAMFileHeader header,
int referenceSequenceIndex,
int alignmentStart,
short readNameLength,
short mappingQuality,
int indexingBin,
int cigarLen,
int flags,
int readLen,
int mateReferenceSequenceIndex,
int mateAlignmentStart,
int insertSize,
byte[] variableLengthBlock)
Create a new BAM Record.
|
BAMRecord |
SAMRecordFactory.createBAMRecord(SAMFileHeader header,
int referenceSequenceIndex,
int alignmentStart,
short readNameLength,
short mappingQuality,
int indexingBin,
int cigarLen,
int flags,
int readLen,
int mateReferenceSequenceIndex,
int mateAlignmentStart,
int insertSize,
byte[] variableLengthBlock)
Create a new BAM Record.
|
SAMRecord |
DefaultSAMRecordFactory.createSAMRecord(SAMFileHeader header)
Create a new SAMRecord to be filled in
|
SAMRecord |
SAMRecordFactory.createSAMRecord(SAMFileHeader header)
Create a new SAMRecord to be filled in
|
void |
SAMTextHeaderCodec.encode(Writer writer,
SAMFileHeader header)
Convert SAMFileHeader from in-memory representation to text representation.
|
void |
SAMTextHeaderCodec.encode(Writer writer,
SAMFileHeader header,
boolean keepExistingVersionNumber)
Convert SAMFileHeader from in-memory representation to text representation.
|
Integer |
SamFileHeaderMerger.getMergedSequenceIndex(SAMFileHeader header,
Integer oldReferenceSequenceIndex)
Another mechanism for getting the new sequence index, for situations in which the reader is not available.
|
String |
SamFileHeaderMerger.getProgramGroupId(SAMFileHeader header,
String originalProgramGroupId) |
String |
SamFileHeaderMerger.getReadGroupId(SAMFileHeader header,
String originalReadGroupId)
Returns the read group id that should be used for the input read and RG id.
|
SAMFileWriter |
SAMFileWriterFactory.makeBAMWriter(SAMFileHeader header,
boolean presorted,
File outputFile)
Create a BAMFileWriter that is ready to receive SAMRecords.
|
SAMFileWriter |
SAMFileWriterFactory.makeBAMWriter(SAMFileHeader header,
boolean presorted,
File outputFile,
int compressionLevel)
Create a BAMFileWriter that is ready to receive SAMRecords.
|
SAMFileWriter |
SAMFileWriterFactory.makeBAMWriter(SAMFileHeader header,
boolean presorted,
OutputStream stream)
Create a BAMFileWriter for writing to a stream that is ready to receive SAMRecords.
|
CRAMFileWriter |
SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader header,
boolean presorted,
File outputFile,
File referenceFasta)
Create a CRAMFileWriter on an output file.
|
CRAMFileWriter |
SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader header,
File outputFile,
File referenceFasta)
Create a CRAMFileWriter on an output file.
|
CRAMFileWriter |
SAMFileWriterFactory.makeCRAMWriter(SAMFileHeader header,
OutputStream stream,
File referenceFasta)
Create a CRAMFileWriter on an output stream.
|
SAMFileWriter |
SAMFileWriterFactory.makeSAMOrBAMWriter(SAMFileHeader header,
boolean presorted,
File outputFile)
Create either a SAM or a BAM writer based on examination of the outputFile extension.
|
SAMFileWriter |
SAMFileWriterFactory.makeSAMWriter(SAMFileHeader header,
boolean presorted,
File outputFile)
Create a SAMTextWriter that is ready to receive SAMRecords.
|
SAMFileWriter |
SAMFileWriterFactory.makeSAMWriter(SAMFileHeader header,
boolean presorted,
OutputStream stream)
Create a SAMTextWriter for writing to a stream that is ready to receive SAMRecords.
|
SAMFileWriter |
SAMFileWriterFactory.makeWriter(SAMFileHeader header,
boolean presorted,
File outputFile,
File referenceFasta)
Create a SAM, BAM or CRAM writer based on examination of the outputFile extension.
|
static void |
BamFileIoUtils.reheaderBamFile(SAMFileHeader samFileHeader,
File inputFile,
File outputFile) |
static void |
BamFileIoUtils.reheaderBamFile(SAMFileHeader samFileHeader,
File inputFile,
File outputFile,
boolean createMd5,
boolean createIndex)
Copy a BAM file but replacing the header
|
protected static Integer |
SAMRecord.resolveIndexFromName(String referenceName,
SAMFileHeader header,
boolean strict)
Static method that resolves and returns the reference index corresponding to a given reference name.
|
protected static String |
SAMRecord.resolveNameFromIndex(int referenceIndex,
SAMFileHeader header)
Static method that resolves and returns the reference name corresponding to a given reference index.
|
void |
SAMFileWriterImpl.setHeader(SAMFileHeader header)
Must be called before addAlignment.
|
void |
SAMRecordSetBuilder.setHeader(SAMFileHeader header) |
void |
SAMRecord.setHeader(SAMFileHeader header)
Sets the SAMFileHeader for this record.
|
void |
SAMRecord.setHeaderStrict(SAMFileHeader header)
Establishes the SAMFileHeader for this record and forces resolution of the record's reference and mate reference
names against the header using the sequence dictionary in the new header.
|
static void |
SamPairUtil.setMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header)
Write the mate info for two SAMRecords.
|
static void |
SamPairUtil.setMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
boolean setMateCigar)
Deprecated.
|
static void |
SamPairUtil.setProperPairAndMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
List<SamPairUtil.PairOrientation> exepectedOrientations)
This method will clear any mate cigar already present.
|
static void |
SamPairUtil.setProperPairAndMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
List<SamPairUtil.PairOrientation> exepectedOrientations,
boolean addMateCigar) |
void |
CRAMContainerStreamWriter.writeHeader(SAMFileHeader header)
Write a CRAM file header and SAM header to the stream.
|
Constructor and Description |
---|
BAMIndexer(File output,
SAMFileHeader fileHeader) |
BAMIndexer(OutputStream output,
SAMFileHeader fileHeader)
Prepare to index a BAM.
|
BAMRecord(SAMFileHeader header,
int referenceID,
int coordinate,
short readNameLength,
short mappingQuality,
int indexingBin,
int cigarLen,
int flags,
int readLen,
int mateReferenceID,
int mateCoordinate,
int insertSize,
byte[] restOfData)
Create a new BAM Record.
|
BAMRecordCodec(SAMFileHeader header) |
BAMRecordCodec(SAMFileHeader header,
SAMRecordFactory factory) |
CRAMContainerStreamWriter(OutputStream outputStream,
OutputStream indexStream,
ReferenceSource source,
SAMFileHeader samFileHeader,
String cramId)
Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM
containers on output stream, with an optional index.
|
CRAMFileWriter(OutputStream outputStream,
OutputStream indexOS,
boolean presorted,
ReferenceSource referenceSource,
SAMFileHeader samFileHeader,
String fileName)
Create a CRAMFileWriter and optional index on output streams.
|
CRAMFileWriter(OutputStream outputStream,
OutputStream indexOS,
ReferenceSource referenceSource,
SAMFileHeader samFileHeader,
String fileName)
Create a CRAMFileWriter and optional index on output streams.
|
CRAMFileWriter(OutputStream outputStream,
ReferenceSource referenceSource,
SAMFileHeader samFileHeader,
String fileName)
Create a CRAMFileWriter on an output stream.
|
CRAMIndexer(File output,
SAMFileHeader fileHeader)
Create a CRAM indexer that writes BAI to a file.
|
CRAMIndexer(OutputStream output,
SAMFileHeader fileHeader)
Create a CRAM indexer that writes BAI to a stream.
|
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
SAMFileHeader header) |
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
SAMFileHeader header,
boolean preSorted) |
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
SAMFileHeader header,
boolean preSorted,
SAMRecordDuplicateComparator comparator)
Allows the user of this iterator to skip the sorting of the input if the input is already sorted.
|
PgIdGenerator(SAMFileHeader header) |
SAMLineParser(SAMFileHeader samFileHeader)
Public constructor.
|
SAMLineParser(SAMFileHeader samFileHeader,
SamReader samFileReader,
File samFile)
Public constructor.
|
SAMLineParser(SAMRecordFactory samRecordFactory,
ValidationStringency validationStringency,
SAMFileHeader samFileHeader,
SamReader samFileReader,
File samFile)
Public constructor.
|
SAMRecord(SAMFileHeader header) |
SRAIndex(SAMFileHeader header,
SRAIterator.RecordRangeInfo recordRangeInfo) |
SRAIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
List<Chunk> chunks) |
Constructor and Description |
---|
SamFileHeaderMerger(SAMFileHeader.SortOrder sortOrder,
Collection<SAMFileHeader> headers,
boolean mergeDictionaries)
Create SAMFileHeader with additional information..
|
SAMRecordDuplicateComparator(List<SAMFileHeader> headers) |
Modifier and Type | Method and Description |
---|---|
static long |
CramIO.writeHeader(Version cramVersion,
OutputStream outStream,
SAMFileHeader samFileHeader,
String cramID)
Write a CRAM File header and a SAM Header to an output stream.
|
Constructor and Description |
---|
ContainerFactory(SAMFileHeader samFileHeader,
int recordsPerSlice) |
ContainerParser(SAMFileHeader samFileHeader) |
Cram2SamRecordFactory(SAMFileHeader header) |
CramNormalizer(SAMFileHeader header,
ReferenceSource referenceSource) |
Sam2CramRecordFactory(byte[] refBases,
SAMFileHeader samFileHeader,
Version version) |
Modifier and Type | Method and Description |
---|---|
SAMFileHeader |
CramHeader.getSamFileHeader()
Get the
SAMFileHeader object associated with this CRAM file header. |
Constructor and Description |
---|
CramHeader(Version version,
String id,
SAMFileHeader samFileHeader)
Create a new
CramHeader object with the specified version, id and SAM file header. |
Constructor and Description |
---|
IntervalFilter(List<Interval> intervals,
SAMFileHeader samHeader)
Prepare to filter out SAMRecords that do not overlap the given list of intervals
|
JavascriptSamRecordFilter(File scriptFile,
SAMFileHeader header)
constructor using a javascript File
|
JavascriptSamRecordFilter(Reader scriptReader,
SAMFileHeader header)
constructor using a java.io.Reader
|
JavascriptSamRecordFilter(String scriptExpression,
SAMFileHeader header)
constructor using a javascript expression
|
Constructor and Description |
---|
ReferenceCache(ngs.ReadCollection run,
SAMFileHeader virtualHeader) |
SRAAlignmentIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
Chunk chunk) |
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
ngs.ReadCollection run,
ngs.AlignmentIterator alignmentIterator,
String readId,
String alignmentId) |
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
ngs.ReadCollection run,
ngs.ReadIterator unalignmentIterator,
String readId,
int unalignedReadFragmentIndex) |
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
String readId,
int unalignedReadFragmentIndex) |
SRALazyRecord(SAMFileHeader header,
SRAAccession accession,
String readId,
String alignmentId) |
SRAUnalignmentIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
SRAIterator.RecordRangeInfo recordRangeInfo,
Chunk chunk) |
Modifier and Type | Method and Description |
---|---|
SAMFileHeader |
IntervalListReferenceSequenceMask.getHeader() |
SAMFileHeader |
IntervalList.getHeader()
Gets the header (if there is one) for the interval list.
|
Modifier and Type | Method and Description |
---|---|
static IntervalList |
IntervalList.fromName(SAMFileHeader header,
String sequenceName)
Creates an IntervalList from the given sequence name
|
Constructor and Description |
---|
IntervalList(SAMFileHeader header)
Constructs a new interval list using the supplied header information.
|
SamRecordTrackingBuffer(int maxRecordsInRam,
int blockSize,
List<File> tmpDirs,
SAMFileHeader header,
Class<T> clazz) |
WholeGenomeReferenceSequenceMask(SAMFileHeader header) |