public class SAMLineParser
extends java.lang.Object
Constructor and Description |
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SAMLineParser(SAMFileHeader samFileHeader)
Public constructor.
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SAMLineParser(SAMFileHeader samFileHeader,
SamReader samFileReader,
java.io.File samFile)
Public constructor.
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SAMLineParser(SAMRecordFactory samRecordFactory,
ValidationStringency validationStringency,
SAMFileHeader samFileHeader,
SamReader samFileReader,
java.io.File samFile)
Public constructor.
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Modifier and Type | Method and Description |
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SAMFileHeader |
getFileHeader()
Get the File header.
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ValidationStringency |
getValidationStringency()
Get validation stringency.
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SAMRecord |
parseLine(java.lang.String line)
Parse a SAM line.
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SAMRecord |
parseLine(java.lang.String line,
int lineNumber)
Parse a SAM line.
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SAMLineParser |
withSamFlagField(SamFlagField samFlagField)
Sets the expected SAM flag type expected for all records.
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public SAMLineParser(SAMFileHeader samFileHeader)
samFileHeader
- SAM file headerpublic SAMLineParser(SAMFileHeader samFileHeader, SamReader samFileReader, java.io.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, java.io.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(java.lang.String line)
line
- line to parsepublic SAMRecord parseLine(java.lang.String line, int lineNumber)
line
- line to parselineNumber
- line number in the file. If the line number is not known
can be <=0.