SAMLineParser (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.SAMLineParser

```
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`.

Constructor Summary

Constructors
Constructor and 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.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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.

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,
                     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,
                     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(String line)
```
    Parse a SAM line.
    
    Parameters:
    
    line - line to parse
    
    Returns:
    
    a new SAMRecord object
  - parseLine
```
public SAMRecord parseLine(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

Class SAMLineParser

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SAMLineParser

SAMLineParser

SAMLineParser

Method Detail

getFileHeader

getValidationStringency

withSamFlagField

parseLine

parseLine