trans.misc
Class ConvertAgilentData

java.lang.Object
  extended bytrans.misc.ConvertAgilentData

public class ConvertAgilentData
extends java.lang.Object

Reads in an Agilent tiling data file and outputs a tpmap and four cela files. Cela files only contain intensities for chromosome mapped oligos, control intensities are set to zero. Agilent uses zero based inter digit numbering, just like UCSC. Assumes each oligo is a 60mer.


Constructor Summary
ConvertAgilentData(java.lang.String[] args)
           
 
Method Summary
static void main(java.lang.String[] args)
           
 boolean parseAgilentFile()
           
static void printDocs()
           
 void processArgs(java.lang.String[] args)
          This method will process each argument and assign new varibles
 boolean save1lq()
           
 boolean saveTPMap()
           
 void writeCelaFiles()
           
 boolean writeSgrFiles()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ConvertAgilentData

public ConvertAgilentData(java.lang.String[] args)
Method Detail

parseAgilentFile

public boolean parseAgilentFile()

writeCelaFiles

public void writeCelaFiles()

writeSgrFiles

public boolean writeSgrFiles()

saveTPMap

public boolean saveTPMap()

save1lq

public boolean save1lq()

processArgs

public void processArgs(java.lang.String[] args)
This method will process each argument and assign new varibles


printDocs

public static void printDocs()

main

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