net.maizegenetics.pangenome.hapCalling

Class VCFMetricsPlugin

net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin

public class VCFMetricsPlugin

This plugin calculates metrics for gvcf files generated from MAFToVCFPlugin. Summary statistics are written to a tab-delimited file, with one row for the full-gvcf summary, and subsequent rows for each chromosome. Metrics include: Number of SNPs, insertions and deletions Number of bases inserted and deleted Total bases Percentage of bases aligned relative to reference - reference blocks and snps are considered to be "aligned" Percentage of bases covered relative to reference - reference, SNPs, and indels are considered to be "covered" (Unmapped ranges are not considered to be "covered") Percentage of reference length inserted and deleted indel sizes mean, quartiles, and largest insertion and deletion sizes mean, quartiles, and largest

Optionally, an additional file can be written containing the sizes of the indels in each gvcf - again separated by chromosome Each line starts with the sample and chromosome name, and then contains a tab-delimited list of indel sizes

Assumptions: gvcf files end with .gvcf, or else are gzipped and end with .gvcf.gz

Constructor Detail

VCFMetricsPlugin

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

This plugin calculates metrics for gvcf files generated from MAFToVCFPlugin. Summary statistics are written to a tab-delimited file, with one row for the full-gvcf summary, and subsequent rows for each chromosome. Metrics include: Number of SNPs, insertions and deletions Number of bases inserted and deleted Total bases Percentage of bases aligned relative to reference - reference blocks and snps are considered to be "aligned" Percentage of bases covered relative to reference - reference, SNPs, and indels are considered to be "covered" (Unmapped ranges are not considered to be "covered") Percentage of reference length inserted and deleted indel sizes mean, quartiles, and largest insertion and deletion sizes mean, quartiles, and largest

Optionally, an additional file can be written containing the sizes of the indels in each gvcf - again separated by chromosome Each line starts with the sample and chromosome name, and then contains a tab-delimited list of indel sizes

Assumptions: gvcf files end with .gvcf, or else are gzipped and end with .gvcf.gz

VCFMetricsPlugin

public VCFMetricsPlugin()

This plugin calculates metrics for gvcf files generated from MAFToVCFPlugin. Summary statistics are written to a tab-delimited file, with one row for the full-gvcf summary, and subsequent rows for each chromosome. Metrics include: Number of SNPs, insertions and deletions Number of bases inserted and deleted Total bases Percentage of bases aligned relative to reference - reference blocks and snps are considered to be "aligned" Percentage of bases covered relative to reference - reference, SNPs, and indels are considered to be "covered" (Unmapped ranges are not considered to be "covered") Percentage of reference length inserted and deleted indel sizes mean, quartiles, and largest insertion and deletion sizes mean, quartiles, and largest

Optionally, an additional file can be written containing the sizes of the indels in each gvcf - again separated by chromosome Each line starts with the sample and chromosome name, and then contains a tab-delimited list of indel sizes

Assumptions: gvcf files end with .gvcf, or else are gzipped and end with .gvcf.gz

Method Detail

processData

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

writeSummaryToFile

public void writeSummaryToFile(@NotNull
                               net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary summary,
                               @NotNull
                               java.io.BufferedWriter writer)

given a vcfsummary object, calculate and write stats to file (see class description for list of stats)

writeIndelsToFile

public void writeIndelsToFile(@NotNull
                              net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary summary,
                              @NotNull
                              java.io.BufferedWriter writer)

write the lengths of indels to file. Deletions represented as negative numbers, insertions positive

getIndelSizeStats

@NotNull
public net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions getIndelSizeStats(@NotNull
                                                                                                             java.util.List<java.lang.Integer> indelSizes)

Given list of indel sizes, return number, mean length, quantiles length, and longest for indels, insertions, and deletions

getVCFStats

@NotNull
public java.util.Map<java.lang.String,net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary> getVCFStats(@NotNull
                                                                                                                               java.io.File file)

Calculates summary statistics for the given gvcf file and returns them as a map

getAllChrVCFStats

@NotNull
public net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary getAllChrVCFStats(@NotNull
                                                                                                     java.util.Map<java.lang.String,net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary> summaries)

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

vcfFile

@Nullable
public java.lang.String vcfFile()

A single .gvcf file (optionally gzipped) to process. Do not include file path, file is assumed to reside within vcfDir

Returns:

vcf file

vcfFile

@NotNull
public VCFMetricsPlugin vcfFile(@NotNull
                                         java.lang.String value)

Set vcf file A single .gvcf file (optionally gzipped) to process. Do not include file path, file is assumed to reside within vcfDir

Parameters:

value - vcf file

Returns:

this plugin

vcfDir

@Nullable
public java.lang.String vcfDir()

vcf directory. Directory containing one or more gvcf files to process It is assumed that files end with .gvcf or .gvcf.gz (if gzipped) All other files in this directory will be ignored.

Returns:

vcf directory

vcfDir

@NotNull
public VCFMetricsPlugin vcfDir(@NotNull
                                        java.lang.String value)

Set vcf directory. vcf directory. Directory containing one or more gvcf files to process It is assumed that files end with .gvcf or .gvcf.gz (if gzipped) All other files in this directory will be ignored.

Parameters:

value - vcf directory

Returns:

this plugin

outFile

@NotNull
public java.lang.String outFile()

output metrics file. The tab-delimited file of summary statistcs calcualted from one or more gvcf files Each file has a summary line in the table, as well as a line for each contig/chromosome

Returns:

output metrics file

outFile

@NotNull
public VCFMetricsPlugin outFile(@NotNull
                                         java.lang.String value)

Set output metrics file output metrics file. The tab-delimited file of summary statistcs calcualted from one or more gvcf files Each file has a summary line in the table, as well as a line for each contig/chromosome

Parameters:

value - output metrics file

Returns:

this plugin

indelFile

@NotNull
public java.lang.String indelFile()

Optional file to write all indel lengths to If not provided, indel lengths will not be written Each line begins with the gvcf and chromosome name (separated by underscore) And then the indel sizes, separated by tabs

Returns:

indel file

indelFile

@NotNull
public VCFMetricsPlugin indelFile(@NotNull
                                           java.lang.String value)

Set indel file Optional file to write all indel lengths to If not provided, indel lengths will not be written Each line begins with the gvcf and chromosome name (separated by underscore) And then the indel sizes, separated by tabs

Parameters:

value - indel file

Returns:

this plugin