net.maizegenetics.pangenome.processAssemblyGenomes

Class AlterNucmerFirstLinePlugin

net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin

public class AlterNucmerFirstLinePlugin

This method created to facilitate changing the first line of the mummer4 nucmer delta files. When a new version of PHG db is being created, and it is using the same reference and same assmebly fastas, the nucmer delta output can be used from the original alignment.

The issue is the first line in this file. That line indicates where the ref and assembly fastas live. When running this in docker vs outside docker, the paths are different. And, if running with a version of docker that mounter to "/tempFileDir/..." vs a newer version that mounts to "/phg/...", the first line doesn't match.

And non-matching lines result in errors when you get to the show-snps and other stages, which are often still run when the nucmer alignment step is skipped.

Constructor Detail

AlterNucmerFirstLinePlugin

public AlterNucmerFirstLinePlugin(@Nullable
                                  java.awt.Frame parentFrame,
                                  boolean isInteractive)

This method created to facilitate changing the first line of the mummer4 nucmer delta files. When a new version of PHG db is being created, and it is using the same reference and same assmebly fastas, the nucmer delta output can be used from the original alignment.

The issue is the first line in this file. That line indicates where the ref and assembly fastas live. When running this in docker vs outside docker, the paths are different. And, if running with a version of docker that mounter to "/tempFileDir/..." vs a newer version that mounts to "/phg/...", the first line doesn't match.

And non-matching lines result in errors when you get to the show-snps and other stages, which are often still run when the nucmer alignment step is skipped.

AlterNucmerFirstLinePlugin

public AlterNucmerFirstLinePlugin()

This method created to facilitate changing the first line of the mummer4 nucmer delta files. When a new version of PHG db is being created, and it is using the same reference and same assmebly fastas, the nucmer delta output can be used from the original alignment.

The issue is the first line in this file. That line indicates where the ref and assembly fastas live. When running this in docker vs outside docker, the paths are different. And, if running with a version of docker that mounter to "/tempFileDir/..." vs a newer version that mounts to "/phg/...", the first line doesn't match.

And non-matching lines result in errors when you get to the show-snps and other stages, which are often still run when the nucmer alignment step is skipped.

Method Detail

processData

@Nullable
public net.maizegenetics.plugindef.DataSet processData(@Nullable
                                                                 net.maizegenetics.plugindef.DataSet input)

changeFile

public void changeFile(@NotNull
                       java.lang.String file,
                       @NotNull
                       java.lang.String justFile,
                       @NotNull
                       java.io.BufferedWriter bw)

convertLine

@NotNull
public java.lang.String convertLine(@NotNull
                                             java.lang.String oldLine)

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

inputDir

@NotNull
public java.lang.String inputDir()

Path for directory holding the files to be changed

Returns:

Input Directory

inputDir

@NotNull
public AlterNucmerFirstLinePlugin inputDir(@NotNull
                                                    java.lang.String value)

Set Input Directory. Path for directory holding the files to be changed

Parameters:

value - Input Directory

Returns:

this plugin

refPath

@NotNull
public java.lang.String refPath()

Path where reference fastas live

Returns:

Reference Path

refPath

@NotNull
public AlterNucmerFirstLinePlugin refPath(@NotNull
                                                   java.lang.String value)

Set Reference Path. Path where reference fastas live

Parameters:

value - Reference Path

Returns:

this plugin

asmPath

@NotNull
public java.lang.String asmPath()

Path where assembly fastas live

Returns:

Assembly Path

asmPath

@NotNull
public AlterNucmerFirstLinePlugin asmPath(@NotNull
                                                   java.lang.String value)

Set Assembly Path. Path where assembly fastas live

Parameters:

value - Assembly Path

Returns:

this plugin

outputDir

@NotNull
public java.lang.String outputDir()

Full Path to which updated files will be written

Returns:

Output Directory

outputDir

@NotNull
public AlterNucmerFirstLinePlugin outputDir(@NotNull
                                                     java.lang.String value)

Set Output Directory. Full Path to which updated files will be written

Parameters:

value - Output Directory

Returns:

this plugin