net.maizegenetics.pangenome.db_loading

Class FindTrimmedAnchorCoordinates

java.lang.Object

net.maizegenetics.pangenome.db_loading.FindTrimmedAnchorCoordinates

public class FindTrimmedAnchorCoordinates
extends Object

NOTE: This version works on the REF only. The assemblies do not have their coordinates in the fasta files - they only have the start, not the end. OH - but I could get it from the length. Due to time, I'm not going to mess this one up. I"ll write another one for assemblies and merge them later. Method takes - a refAnchor fasta file, (I dumped reference anchors from the pre-trimmed db) - a list of files from a directory that contain the trimmed versions on a per-anchor basis. Find the start and end of the trimmed sequence in the ref sequence. The start is where it matches. The end is the length of the trimmed sequence added to the start. Output: The important output is the csv file that will be used to load the new reference anchors to the "trimmed" database.

Author:

lcj34

Constructor Summary

Constructors

Constructor and Description
FindTrimmedAnchorCoordinates()

Method Summary

Modifier and Type	Method and Description
static void	main(String[] args)
static void	processMain(String refFasta, Map<Integer,String> trimmedFastas, String outputDir, String lineName)

Methods inherited from class java.lang.Object

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

Constructor Detail

FindTrimmedAnchorCoordinates

public FindTrimmedAnchorCoordinates()

Method Detail

processMain

public static void processMain(String refFasta,
                               Map<Integer,String> trimmedFastas,
                               String outputDir,
                               String lineName)

main

public static void main(String[] args)

Parameters:

args -