net.maizegenetics.pangenome.db_loading

Class FindTrimmedAssemblyCoordinates

java.lang.Object

net.maizegenetics.pangenome.db_loading.FindTrimmedAssemblyCoordinates

public class FindTrimmedAssemblyCoordinates
extends Object

THis file is similar to FindTrimmedAnchorCoordinates used for the reference. The difference is the ref has all anchors. Assemblies do not. We need to read the assembly fasta, determine which anchor is represented The anchor is there in the idLine - the last value after the space, e.g. >1:44289:49837;chr1:1 1 THis is creating a fasta, but it isn't useful because the IDline is not what is needed when loading into the DB. Idline must have >B73RefChrom:B73startpos:B73EndPos;assemblyChrom:assemblyStart:asemblyEnd anchorid

Author:

lcj34

Constructor Summary

Constructors

Constructor and Description
FindTrimmedAssemblyCoordinates()

Method Summary

Modifier and Type	Method and Description
static void	main(String[] args)
static void	processMain(String assemblyFasta, 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

FindTrimmedAssemblyCoordinates

public FindTrimmedAssemblyCoordinates()

Method Detail

processMain

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

main

public static void main(String[] args)

Parameters:

args -