net.maizegenetics.pangenome.processAssemblyGenomes

Class ScorePafFileByNMThresholdPlugin

net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPlugin

public class ScorePafFileByNMThresholdPlugin

Plugin to score a PAF file by different NM(Edit Distance) thresholds.

In PAF files, NM means the number of edits for that alignment. We are looking for a percentage of edit distance over the length of the aligned region.

For each line in the PAF file, the aligned number of 'contig' coordinates is compared to the edit distance. If NM/numSites < our current NMthreshold, that aligned region is loaded into a RangeSet. The RangeSet will merge any overlapping regions. Then once all the mappings have been processed, this walks through each contig and determines how many of the bps of the full contig were mapped with a good enough NM. These values are output to a file created in outputDir.

This plugin allows you to run multiple NM thresholds to get an overall idea of how well things map.

Constructor Detail

ScorePafFileByNMThresholdPlugin

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

Plugin to score a PAF file by different NM(Edit Distance) thresholds.

In PAF files, NM means the number of edits for that alignment. We are looking for a percentage of edit distance over the length of the aligned region.

For each line in the PAF file, the aligned number of 'contig' coordinates is compared to the edit distance. If NM/numSites < our current NMthreshold, that aligned region is loaded into a RangeSet. The RangeSet will merge any overlapping regions. Then once all the mappings have been processed, this walks through each contig and determines how many of the bps of the full contig were mapped with a good enough NM. These values are output to a file created in outputDir.

This plugin allows you to run multiple NM thresholds to get an overall idea of how well things map.

Method Detail

processData

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

For each line in the PAF file, the aligned number of 'contig' coordinates is compared to the edit distance. If NM/numSites < our current NMthreshold, that aligned region is loaded into a RangeSet. The RangeSet will merge any overlapping regions. Then once all the mappings have been processed, this walks through each contig and determines how many of the bps of the full contig were mapped with a good enough NM. These values are output to a file created in outputDir.

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

inputPAFFile

@NotNull
public java.lang.String inputPAFFile()

Input PAF file

Returns:

Input PAF file

inputPAFFile

@NotNull
public ScorePafFileByNMThresholdPlugin inputPAFFile(@NotNull
                                                             java.lang.String value)

Set Input PAF file. Input PAF file

Parameters:

value - Input PAF file

Returns:

this plugin

outputDir

@NotNull
public java.lang.String outputDir()

Directory to output the processed PAF files

Returns:

Output Directory

outputDir

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

Set Output Directory. Directory to output the processed PAF files

Parameters:

value - Output Directory

Returns:

this plugin

editDistanceThresholds

@NotNull
public java.lang.String editDistanceThresholds()

Edit distance thresholds separated by comma's

Returns:

NMThresholds

editDistanceThresholds

@NotNull
public ScorePafFileByNMThresholdPlugin editDistanceThresholds(@NotNull
                                                                       java.lang.String value)

Set NMThresholds. Edit distance thresholds separated by comma's

Parameters:

value - NMThresholds

Returns:

this plugin