nix.affy.bpmap
Class MummerFilter

java.lang.Object
  nix.affy.bpmap.MummerFilter

public class MummerFilter

extends java.lang.Object

Application to remap and filter a ProbeExporter text bpmap file for exact matches useing MUMMER.

Constructor Summary

MummerFilter(java.lang.String[] args)

Method Summary

boolean	appendMummerHits() Runs through mummer results and appends any hits to probeExporterFile.
void	buildBPMap() Builds a bpmap file from a mummer results file
java.lang.String[]	fetchMMCoordinates(java.lang.String pmX, java.lang.String pmY)
java.util.ArrayList	fetchSameNumberLines(java.io.BufferedReader lines)
static void	main(java.lang.String[] args)
java.io.File	makeFastaFile() Makes a fasta file from a probExporterBPMapFile
static void	printDocs()
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles
boolean	runMummerExactMatcher(java.io.File genomeFastaFile) Runs MUMMER to find perfect matches

Methods inherited from class java.lang.Object

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

Constructor Detail

MummerFilter

public MummerFilter(java.lang.String[] args)

Method Detail

appendMummerHits

public boolean appendMummerHits()

Runs through mummer results and appends any hits to probeExporterFile. If multiple hits then it strips the line.

buildBPMap

public void buildBPMap()

Builds a bpmap file from a mummer results file

fetchMMCoordinates

public java.lang.String[] fetchMMCoordinates(java.lang.String pmX,
                                             java.lang.String pmY)

fetchSameNumberLines

public java.util.ArrayList fetchSameNumberLines(java.io.BufferedReader lines)

runMummerExactMatcher

public boolean runMummerExactMatcher(java.io.File genomeFastaFile)

Runs MUMMER to find perfect matches

makeFastaFile

public java.io.File makeFastaFile()

Makes a fasta file from a probExporterBPMapFile

main

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

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign any new varibles

printDocs

public static void printDocs()