net.maizegenetics.pangenome.hapCalling

Class SimulatedReadsPlugin

net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin

public class SimulatedReadsPlugin

Constructor Detail

SimulatedReadsPlugin

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

Method Detail

processData

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

simulateSingleReadsForTaxon

@NotNull
public java.lang.String simulateSingleReadsForTaxon(@NotNull
                                                             java.lang.String taxonName,
                                                             @NotNull
                                                             HaplotypeGraph myGraph)

simulatePairedEndReadsForTaxon

@NotNull
public kotlin.Pair<java.lang.String,java.lang.String> simulatePairedEndReadsForTaxon(@NotNull
                                                                                              java.lang.String taxonName,
                                                                                              @NotNull
                                                                                              HaplotypeGraph myGraph)

getToolTipText

@NotNull
public java.lang.String getToolTipText()

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

createSingleReads

@NotNull
public java.lang.String createSingleReads(@NotNull
                                                   java.lang.String sequence,
                                                   double depth,
                                                   int readLength,
                                                   int hapid)

createPairedEndReads

@NotNull
public java.util.List<java.lang.String> createPairedEndReads(@NotNull
                                                                      java.lang.String sequence,
                                                                      double depth,
                                                                      int readLength,
                                                                      int insertSize,
                                                                      int hapid)

reverseCompliment

@NotNull
public java.lang.String reverseCompliment(@NotNull
                                                   java.lang.String seq)

coverage

public double coverage()

average coverage of reads for a reference range

Returns:

Coverage

coverage

@NotNull
public SimulatedReadsPlugin coverage(double value)

Set Coverage. average coverage of reads for a reference range

Parameters:

value - Coverage

Returns:

this plugin

lineName

@Nullable
public java.lang.String lineName()

the name of the line for which reads will be simulated. If not specified, all lines will be simulated for the haplotype method.

Returns:

Line Name

lineName

@NotNull
public SimulatedReadsPlugin lineName(@NotNull
                                              java.lang.String value)

Set Line Name. the name of the line for which reads will be simulated. If not specified, all lines will be simulated for the haplotype method.

Parameters:

value - Line Name

Returns:

this plugin

haplotypeMethod

@NotNull
public java.lang.String haplotypeMethod()

the haplotype method used to simulate reads

Returns:

Haplotype Method

haplotypeMethod

@NotNull
public SimulatedReadsPlugin haplotypeMethod(@NotNull
                                                     java.lang.String value)

Set Haplotype Method. the haplotype method used to simulate reads

Parameters:

value - Haplotype Method

Returns:

this plugin

fastqDir

@NotNull
public java.lang.String fastqDir()

the directory to which the simulated read fastq will be written. The default will write to a temp directory, which will not be available after the plugin finishes.

Returns:

Fastq Dir

fastqDir

@NotNull
public SimulatedReadsPlugin fastqDir(@NotNull
                                              java.lang.String value)

Set Fastq Dir. the directory to which the simulated read fastq will be written. The default will write to a temp directory, which will not be available after the plugin finishes.

Parameters:

value - Fastq Dir

Returns:

this plugin

pairedEnd

public boolean pairedEnd()

Should paired end reads be generated?

Returns:

Paired End

pairedEnd

@NotNull
public SimulatedReadsPlugin pairedEnd(boolean value)

Set Paired End. Should paired end reads be generated?

Parameters:

value - Paired End

Returns:

this plugin

readLength

public int readLength()

length of reads to be generated

Returns:

Read Length

readLength

@NotNull
public SimulatedReadsPlugin readLength(int value)

Set Read Length. length of reads to be generated

Parameters:

value - Read Length

Returns:

this plugin

insertLength

public int insertLength()

for paired end reads the number of base pairs between reads

Returns:

Insert Length

insertLength

@NotNull
public SimulatedReadsPlugin insertLength(int value)

Set Insert Length. for paired end reads the number of base pairs between reads

Parameters:

value - Insert Length

Returns:

this plugin