public class SAMLineParser extends Object
Constructor | Description |
---|---|
SAMLineParser(SAMFileHeader samFileHeader) |
Public constructor.
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SAMLineParser(SAMFileHeader samFileHeader,
SamReader samFileReader,
File samFile) |
Public constructor.
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SAMLineParser(SAMRecordFactory samRecordFactory,
ValidationStringency validationStringency,
SAMFileHeader samFileHeader,
SamReader samFileReader,
File samFile) |
Public constructor.
|
Modifier and Type | Method | Description |
---|---|---|
SAMFileHeader |
getFileHeader() |
Get the File header.
|
ValidationStringency |
getValidationStringency() |
Get validation stringency.
|
SAMRecord |
parseLine(String line) |
Parse a SAM line.
|
SAMRecord |
parseLine(String line,
int lineNumber) |
Parse a SAM line.
|
SAMLineParser |
withSamFlagField(SamFlagField samFlagField) |
Sets the expected SAM flag type expected for all records.
|
public SAMLineParser(SAMFileHeader samFileHeader)
samFileHeader
- SAM file headerpublic SAMLineParser(SAMFileHeader samFileHeader, SamReader samFileReader, File samFile)
samFileHeader
- SAM file headersamFileReader
- SAM file reader For passing to SAMRecord.setFileSource, may be null.samFile
- SAM file being read (for error message only, may be null)public SAMLineParser(SAMRecordFactory samRecordFactory, ValidationStringency validationStringency, SAMFileHeader samFileHeader, SamReader samFileReader, File samFile)
samRecordFactory
- SamRecord FactoryvalidationStringency
- validation stringencysamFileHeader
- SAM file headersamFileReader
- SAM file reader For passing to SAMRecord.setFileSource, may be null.samFile
- SAM file being read (for error message only, may be null)public SAMFileHeader getFileHeader()
public ValidationStringency getValidationStringency()
public SAMLineParser withSamFlagField(SamFlagField samFlagField)
public SAMRecord parseLine(String line)
line
- line to parse