broad.pda.seq.rap.CountProbes Class Reference

Inheritance diagram for broad.pda.seq.rap.CountProbes:

Collaboration diagram for broad.pda.seq.rap.CountProbes:

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

Public Attributes
File	INPUT
File	OUTPUT
File	STATS
Integer	T7BASES = 26
Integer	OVERLAP = 5

Static Public Attributes
static final int	ORIGINAL_ARRAY_LEFT = 30
static final int	ORIGINAL_ARRAY_RIGHT = 20
static final int	MAIN_ARRAY_LEFT = 30
static final int	MAIN_ARRAY_RIGHT = 30
static final int	SIMPLE_ARRAY_LEFT = 15
static final int	SIMPLE_ARRAY_RIGHT = 15
static final int	ARRAY_140105 = 17
static final int	MRNA_ARRAY_LEFT = 40
static final int	MRNA_ARRAY_RIGHT = 40

Protected Member Functions
int	doWork ()

Detailed Description

Program to find read pairs in which one of the pairs aligns to at least part of the qPCR tag sequence of the probe. Input SAM files have been aligned to the full probe sequences (including the target sequence, e.g. of Xist).

Author

engreitz

Member Function Documentation

int broad.pda.seq.rap.CountProbes.doWork ( )

protected

static void broad.pda.seq.rap.CountProbes.main ( final String[]  args )

static

Stock main method.

Parameters

args	main arguments

Member Data Documentation

final int broad.pda.seq.rap.CountProbes.ARRAY_140105 = 17

static

File broad.pda.seq.rap.CountProbes.INPUT

final int broad.pda.seq.rap.CountProbes.MAIN_ARRAY_LEFT = 30

static

final int broad.pda.seq.rap.CountProbes.MAIN_ARRAY_RIGHT = 30

static

final int broad.pda.seq.rap.CountProbes.MRNA_ARRAY_LEFT = 40

static

final int broad.pda.seq.rap.CountProbes.MRNA_ARRAY_RIGHT = 40

static

final int broad.pda.seq.rap.CountProbes.ORIGINAL_ARRAY_LEFT = 30

static

final int broad.pda.seq.rap.CountProbes.ORIGINAL_ARRAY_RIGHT = 20

static

File broad.pda.seq.rap.CountProbes.OUTPUT

Integer broad.pda.seq.rap.CountProbes.OVERLAP = 5

final int broad.pda.seq.rap.CountProbes.SIMPLE_ARRAY_LEFT = 15

static

final int broad.pda.seq.rap.CountProbes.SIMPLE_ARRAY_RIGHT = 15

static

File broad.pda.seq.rap.CountProbes.STATS

Integer broad.pda.seq.rap.CountProbes.T7BASES = 26

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

• java/broad/pda/seq/rap/CountProbes.java