broad.pda.samtools.SAMFragmentWriter Class Reference

Public Member Functions
	SAMFragmentWriter (String input, String output) throws IOException
	SAMFragmentWriter (String input, String output, String samHeader) throws IOException

Static Public Member Functions
static String	getSamString (SAMRecord rec)
static void	main (String[] args) throws IOException

Detailed Description

Author

prussell

Constructor & Destructor Documentation

broad.pda.samtools.SAMFragmentWriter.SAMFragmentWriter	(	String	input,
		String	output
	)		throws IOException

Parameters

input	Input sam or bam file
output	Output bam file

Exceptions

IOException

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broad.pda.samtools.SAMFragmentWriter.SAMFragmentWriter	(	String	input,
		String	output,
		String	samHeader
	)		throws IOException

Parameters

input	Input sam or bam file
output	Output bam file
samHeader	Optional sam header if header is too large for SAMFileHeader object

Exceptions

IOException

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Member Function Documentation

static String broad.pda.samtools.SAMFragmentWriter.getSamString ( SAMRecord  rec )

static

Get sam line for record

Parameters

rec	The record

Returns

Sam formatted line ending in newline

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static void broad.pda.samtools.SAMFragmentWriter.main ( String[]  args ) throws IOException

static

Parameters

args

Exceptions

IOException

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The documentation for this class was generated from the following file:

• java/broad/pda/samtools/SAMFragmentWriter.java