htsjdk.samtools

Class SAMLineParser

java.lang.Object

htsjdk.samtools.SAMLineParser

public class SAMLineParser
extends java.lang.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`.

Constructor Summary

Constructors

Constructor and Description
SAMLineParser(SAMFileHeader samFileHeader) Public constructor.
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.

Method Summary

Modifier and Type	Method and Description
SAMFileHeader	getFileHeader() Get the File header.
ValidationStringency	getValidationStringency() Get validation stringency.
SAMRecord	parseLine(java.lang.String line) Parse a SAM line.
SAMRecord	parseLine(java.lang.String line, int lineNumber) Parse a SAM line.
SAMLineParser	withSamFlagField(SamFlagField samFlagField) Sets the expected SAM flag type expected for all records.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SAMLineParser

public SAMLineParser(SAMFileHeader samFileHeader)

Public constructor. Use the default SAMRecordFactory and stringency.

Parameters:

samFileHeader - SAM file header

SAMLineParser

public SAMLineParser(SAMFileHeader samFileHeader,
                     SamReader samFileReader,
                     java.io.File samFile)

Public constructor. Use the default SAMRecordFactory and stringency.

Parameters:

samFileHeader - SAM file header

samFileReader - SAM file reader For passing to SAMRecord.setFileSource, may be null.

samFile - SAM file being read (for error message only, may be null)

SAMLineParser

public SAMLineParser(SAMRecordFactory samRecordFactory,
                     ValidationStringency validationStringency,
                     SAMFileHeader samFileHeader,
                     SamReader samFileReader,
                     java.io.File samFile)

Public constructor.

Parameters:

samRecordFactory - SamRecord Factory

validationStringency - validation stringency

samFileHeader - SAM file header

samFileReader - SAM file reader For passing to SAMRecord.setFileSource, may be null.

samFile - SAM file being read (for error message only, may be null)

Method Detail

getFileHeader

public SAMFileHeader getFileHeader()

Get the File header.

Returns:

the SAM file header

getValidationStringency

public ValidationStringency getValidationStringency()

Get validation stringency.

Returns:

validation stringency

withSamFlagField

public SAMLineParser withSamFlagField(SamFlagField samFlagField)

Sets the expected SAM flag type expected for all records.

parseLine

public SAMRecord parseLine(java.lang.String line)

Parse a SAM line.

Parameters:

line - line to parse

Returns:

a new SAMRecord object

parseLine

public SAMRecord parseLine(java.lang.String line,
                           int lineNumber)

Parse a SAM line.

Parameters:

line - line to parse

lineNumber - line number in the file. If the line number is not known can be <=0.

Returns:

a new SAMRecord object