broad.pda.samtools.FilterPairedReadsByMAQ Class Reference

Inheritance diagram for broad.pda.samtools.FilterPairedReadsByMAQ:

Collaboration diagram for broad.pda.samtools.FilterPairedReadsByMAQ:

Static Public Member Functions
static void	main (final String[] args)

Public Attributes
File	INPUT
Integer	MINIMUM_MAPPING_QUALITY = 30
File	OUTPUT
Boolean	REMOVE_MATE = false
File	METRICS =null
SAMFileHeader.SortOrder	SORT_ORDER = SAMFileHeader.SortOrder.coordinate

Protected Member Functions
int	doWork ()

Detailed Description

Author

engreitz Remove reads that do not map uniquely to the genome. If a read's mate is removed this way, mark that read as unpaired.

Member Function Documentation

int broad.pda.samtools.FilterPairedReadsByMAQ.doWork ( )

protected

static void broad.pda.samtools.FilterPairedReadsByMAQ.main ( final String[]  args )

static

Stock main method.

Parameters

args	main arguments

Member Data Documentation

File broad.pda.samtools.FilterPairedReadsByMAQ.INPUT

File broad.pda.samtools.FilterPairedReadsByMAQ.METRICS =null

Integer broad.pda.samtools.FilterPairedReadsByMAQ.MINIMUM_MAPPING_QUALITY = 30

File broad.pda.samtools.FilterPairedReadsByMAQ.OUTPUT

Boolean broad.pda.samtools.FilterPairedReadsByMAQ.REMOVE_MATE = false

SAMFileHeader.SortOrder broad.pda.samtools.FilterPairedReadsByMAQ.SORT_ORDER = SAMFileHeader.SortOrder.coordinate

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

• java/broad/pda/samtools/FilterPairedReadsByMAQ.java