net.maizegenetics.pangenome.hapCalling

Class SAMToMappingPlugin

net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin

public class SAMToMappingPlugin

Plugin to take mapped reads to the pangenome in a SAM file and prepare and upload the ReadMappings to the DB.

This plugin uses a Keyfile containing the following columns: cultivar, flowcell_lane, filename, and PlateID It will then walk through each entry in the keyfile and will attempt to prepare the SAM file to create ReadMappings

A number of filtering steps are done to improve the quality of the information stored in the db.

Only equally optimal mappings(By Edit Distance(NM) are kept)

Additional filtering is done to remove reads which are unmapped or clipped

If running in paired mode, the reads must be on opposite strands and both must currently hit the same haplotype in a single reference range.

Optimal mappings across reference ranges are processed, but reads are only assigned to haplotypes in the reference range with the most hits(providing that at least 1- maxRefRangeError percentage hit that refRange) Based on testing, this seems to be working the best to balance #of reads used with accuracy.

Constructor Detail

SAMToMappingPlugin

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

Plugin to take mapped reads to the pangenome in a SAM file and prepare and upload the ReadMappings to the DB.

This plugin uses a Keyfile containing the following columns: cultivar, flowcell_lane, filename, and PlateID It will then walk through each entry in the keyfile and will attempt to prepare the SAM file to create ReadMappings

A number of filtering steps are done to improve the quality of the information stored in the db.

Only equally optimal mappings(By Edit Distance(NM) are kept)

Additional filtering is done to remove reads which are unmapped or clipped

If running in paired mode, the reads must be on opposite strands and both must currently hit the same haplotype in a single reference range.

Optimal mappings across reference ranges are processed, but reads are only assigned to haplotypes in the reference range with the most hits(providing that at least 1- maxRefRangeError percentage hit that refRange) Based on testing, this seems to be working the best to balance #of reads used with accuracy.

Method Detail

processData

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

runGraphlessSamToMapping

public void runGraphlessSamToMapping()

This function will run the SAM -> ReadMapping File portion of the pipeline without needing DB access or a graph input.

runGraphSamToMapping

public void runGraphSamToMapping(@NotNull
                                 HaplotypeGraph graph)

This function will run the SAM -> ReadMapping File portion of the pipeline and will write to the DB.

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

keyFile

@NotNull
public java.lang.String keyFile()

Name of the Keyfile to process. Must have columns cultivar, flowcell_lane, filename, and PlateID. Optionally for paired end reads, filename2 is needed. If filename2 is not supplied, Minimap2 will run in single end mode. Otherwise will be paired.

Returns:

keyFile

keyFile

@NotNull
public SAMToMappingPlugin keyFile(@NotNull
                                           java.lang.String value)

Set keyFile. Name of the Keyfile to process. Must have columns cultivar, flowcell_lane, filename, and PlateID. Optionally for paired end reads, filename2 is needed. If filename2 is not supplied, Minimap2 will run in single end mode. Otherwise will be paired.

Parameters:

value - keyFile

Returns:

this plugin

samDir

@NotNull
public java.lang.String samDir()

Name of the SAM/BAM dir to process.

Returns:

SAM/BAM dir to process

samDir

@NotNull
public SAMToMappingPlugin samDir(@NotNull
                                          java.lang.String value)

Set SAM/BAM dir to process. Name of the SAM/BAM dir to process.

Parameters:

value - SAM/BAM dir to process

Returns:

this plugin

maxRefRangeError

public double maxRefRangeError()

Maximum allowed error when choosing best reference range to count. Error is computed 1 - (mostHitRefCount/totalHits)

Returns:

Max Ref Range Err

maxRefRangeError

@NotNull
public SAMToMappingPlugin maxRefRangeError(double value)

Set Max Ref Range Err. Maximum allowed error when choosing best reference range to count. Error is computed 1

• (mostHitRefCount/totalHits)

Parameters:

value - Max Ref Range Err

Returns:

this plugin

lowMemMode

public boolean lowMemMode()

Run in low memory mode.

Returns:

Low Mem Mode

lowMemMode

@NotNull
public SAMToMappingPlugin lowMemMode(boolean value)

Set Low Mem Mode. Run in low memory mode.

Parameters:

value - Low Mem Mode

Returns:

this plugin

methodName

@NotNull
public java.lang.String methodName()

Method name to be stored in the DB.

Returns:

Method Name

methodName

@NotNull
public SAMToMappingPlugin methodName(@NotNull
                                              java.lang.String value)

Set Method Name. Method name to be stored in the DB.

Parameters:

value - Method Name

Returns:

this plugin

methodDescription

@NotNull
public java.lang.String methodDescription()

Method description to be stored in the DB.

Returns:

Method Description

methodDescription

@NotNull
public SAMToMappingPlugin methodDescription(@NotNull
                                                     java.lang.String value)

Set Method Description. Method description to be stored in the DB.

Parameters:

value - Method Description

Returns:

this plugin

outputDebugDir

@NotNull
public java.lang.String outputDebugDir()

Directory to write out the read mapping files. This is optional for debug purposes.

Returns:

Debug Directory to write out read Mapping files.

outputDebugDir

@NotNull
public SAMToMappingPlugin outputDebugDir(@NotNull
                                                  java.lang.String value)

Set Debug Directory to write out read Mapping files.. Directory to write out the read mapping files. This is optional for debug purposes.

Parameters:

value - Debug Directory to write out read Mapping files.

Returns:

this plugin

outputSecondaryMappingStats

public boolean outputSecondaryMappingStats()

Ouptput Secondary Mapping Statistics such as total AS for each haplotype ID

Returns:

Output secondary mapping statistics.

outputSecondaryMappingStats

@NotNull
public SAMToMappingPlugin outputSecondaryMappingStats(boolean value)

Set Output secondary mapping statistics.. Ouptput Secondary Mapping Statistics such as total AS for each haplotype ID

Parameters:

value - Output secondary mapping statistics.

Returns:

this plugin

isTestMethod

public boolean isTestMethod()

Indication if the data is to be loaded against a test method. Data loaded with test methods are not cached with the PHG ktor server

Returns:

Is Test Method

isTestMethod

@NotNull
public SAMToMappingPlugin isTestMethod(boolean value)

Set Is Test Method. Indication if the data is to be loaded against a test method. Data loaded with test methods are not cached with the PHG ktor server

Parameters:

value - Is Test Method

Returns:

this plugin

updateDB

public boolean updateDB()

If set to true, the read mappings will be written to the db. Otherwise nothing will be written.

Returns:

Update D B

updateDB

@NotNull
public SAMToMappingPlugin updateDB(boolean value)

Set Update D B. If set to true, the read mappings will be written to the db. Otherwise nothing will be written.

Parameters:

value - Update D B

Returns:

this plugin

runWithoutGraph

public boolean runWithoutGraph()

If set to true, will require the input of a JSON file created by CreateHapIdMapsPlugin and will got require a Graph object input.

Returns:

Run Without Graph

runWithoutGraph

@NotNull
public SAMToMappingPlugin runWithoutGraph(boolean value)

Set Run Without Graph. If set to true, will require the input of a JSON file created by CreateHapIdMapsPlugin and will got require a Graph object input.

Parameters:

value - Run Without Graph

Returns:

this plugin

hapIdMapFile

@NotNull
public java.lang.String hapIdMapFile()

Location of the HapIdMapFile where the graph Information can be found.

Returns:

Hap Id Map File

hapIdMapFile

@NotNull
public SAMToMappingPlugin hapIdMapFile(@NotNull
                                                java.lang.String value)

Set Hap Id Map File. Location of the HapIdMapFile where the graph Information can be found.

Parameters:

value - Hap Id Map File

Returns:

this plugin

inputFile

@NotNull
public java.lang.String inputFile()

Input SAM file to be run through. If this is not set it will run everything in the inputDir

Returns:

Input S A M File

inputFile

@NotNull
public SAMToMappingPlugin inputFile(@NotNull
                                             java.lang.String value)

Set Input S A M File. Input SAM file to be run through. If this is not set it will run everything in the inputDir

Parameters:

value - Input S A M File

Returns:

this plugin