trans.tpmap
Class MummerMapper

java.lang.Object
  trans.tpmap.MummerMapper

public class MummerMapper

extends java.lang.Object

Application to map 1lq files to fasta files. Uses Mummer to map oligos to the fasta files. Reverses the oligo sequences in the 1lq file prior to mapping with Mummer.

Field Summary

static java.lang.String

controlChromosomeName String given to naming the control sequences.

Constructor Summary

MummerMapper(java.lang.String[] args)

Method Summary

boolean	appendMummerHits() Runs through mummer results and appends any hits to filtered1lq
void	buildTPMap() Builds a tpmap file from a mummer results file
java.util.ArrayList	fetchSameNumberLines(java.io.BufferedReader lines, int oligoLength) Loads the mummer results for one oligo into an ArrayList.
static void	main(java.lang.String[] args)
void	makeFastaAndFilter() Makes a fasta file from a 1lq file, reverses the sequence of each oligo, drops control probes
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

Field Detail

controlChromosomeName

public static final java.lang.String controlChromosomeName

String given to naming the control sequences.

See Also:

Constant Field Values

Constructor Detail

MummerMapper

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

Method Detail

appendMummerHits

public boolean appendMummerHits()

Runs through mummer results and appends any hits to filtered1lq

buildTPMap

public void buildTPMap()

Builds a tpmap file from a mummer results file

fetchSameNumberLines

public java.util.ArrayList fetchSameNumberLines(java.io.BufferedReader lines,
                                                int oligoLength)

Loads the mummer results for one oligo into an ArrayList. Checks each mummer hit to ensure it is equal to the oligo length. No partial matches.

runMummerExactMatcher

public boolean runMummerExactMatcher(java.io.File genomeFastaFile)

Runs MUMMER to find perfect matches

makeFastaAndFilter

public void makeFastaAndFilter()

Makes a fasta file from a 1lq file, reverses the sequence of each oligo, drops control probes

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()