Package htsjdk.samtools
Class SAMLineParser
- java.lang.Object
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- htsjdk.samtools.SAMLineParser
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public class SAMLineParser extends Object
This class enables creation of a SAMRecord object from a String in SAM text format. The SAM flag field will be inferred for each record separately, unless the expected format is set using `withSamFlagField`.
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Constructor Summary
Constructors Constructor Description 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.
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Method Summary
All Methods Instance Methods Concrete Methods 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.
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Constructor Detail
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SAMLineParser
public SAMLineParser(SAMFileHeader samFileHeader)
Public constructor. Use the default SAMRecordFactory and stringency.- Parameters:
samFileHeader
- SAM file header
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SAMLineParser
public SAMLineParser(SAMFileHeader samFileHeader, SamReader samFileReader, File samFile)
Public constructor. Use the default SAMRecordFactory and stringency.- Parameters:
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)
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SAMLineParser
public SAMLineParser(SAMRecordFactory samRecordFactory, ValidationStringency validationStringency, SAMFileHeader samFileHeader, SamReader samFileReader, File samFile)
Public constructor.- Parameters:
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)
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Method Detail
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getFileHeader
public SAMFileHeader getFileHeader()
Get the File header.- Returns:
- the SAM file header
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getValidationStringency
public ValidationStringency getValidationStringency()
Get validation stringency.- Returns:
- validation stringency
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withSamFlagField
public SAMLineParser withSamFlagField(SamFlagField samFlagField)
Sets the expected SAM flag type expected for all records.
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parseLine
public SAMRecord parseLine(String line)
Parse a SAM line.- Parameters:
line
- line to parse- Returns:
- a new SAMRecord object
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