Class ConvertToExonFormat

java.lang.Object
  ConvertToExonFormat

public class ConvertToExonFormat
extends java.lang.Object

File Format of output (tab delimited) chromosome exonStart exonEnd geneName FPKM/coverage SNP levels/BAF .pileup -> .exon

Author:

arthiramachandran

Field Summary

(package private) static java.util.ArrayList<java.lang.Integer>	chromosomes
(package private) static java.lang.String	exonCaptureArrayFileName
(package private) static java.util.ArrayList<Exon>	Exons
(package private) static java.lang.String	mappedReadsFileName
(package private) static java.lang.String	outputFileName
(package private) static boolean	printTimingMetrics
(package private) static boolean	usingPileup

Constructor Summary

ConvertToExonFormat()

Method Summary

static void	main(java.lang.String[] args)
private static void	parseArguments(java.lang.String[] arguments) Parses arguments to program

Methods inherited from class java.lang.Object

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

Field Detail

Exons

static java.util.ArrayList<Exon> Exons

exonCaptureArrayFileName

static java.lang.String exonCaptureArrayFileName

mappedReadsFileName

static java.lang.String mappedReadsFileName

outputFileName

static java.lang.String outputFileName

chromosomes

static java.util.ArrayList<java.lang.Integer> chromosomes

printTimingMetrics

static boolean printTimingMetrics

usingPileup

static boolean usingPileup

Constructor Detail

ConvertToExonFormat

public ConvertToExonFormat()

Method Detail

main

public static void main(java.lang.String[] args)

parseArguments

private static void parseArguments(java.lang.String[] arguments)

Parses arguments to program

Parameters:

arguments - list of arguments