net.maizegenetics.pangenome.db_loading

Class LoadHaplotypesFromGVCFPlugin

net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin

public class LoadHaplotypesFromGVCFPlugin

Plugin to load up a list of GVCF files given an input keyfile.

This plugin will open up the key file and loop through each record loading up the db.

TODO work on multithreading this process for speed increases.

Constructor Detail

LoadHaplotypesFromGVCFPlugin

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

Plugin to load up a list of GVCF files given an input keyfile.

This plugin will open up the key file and loop through each record loading up the db.

TODO work on multithreading this process for speed increases.

Method Detail

processData

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

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

wGSKeyFile

@NotNull
public java.lang.String wGSKeyFile()

Keyfile used to specify the inputs to the DB. Must have columns sample_name, files, type, chrPhased, genePhased, phasingConf and gvcfServerPath. Optionally you can have sample_description, assemblyServerPath, assemblyLocalPath. Ordering of the columns does not matter. sample_name is the name of the taxon you are uploading. files is a comma-separated list of file names(without path) providing the names of the GVCF files to be uploaded. If there are multiple files, gamete_ids will be assigned in order. type is the type of the files. To use this for this Plugin GVCF needs to be specified.chrPhased and genePhased must be either 'true' or 'false' and represent if the chromosome or the genes are phased or not phasingConf must be a number between 0.0 and 1.0 representing the confidence in the phasing. sample_description to provide a short description of the sample name to be uploaded. If this column is not specified an empty description will be used. optional: assemblyServerPath is an external server and path where the genome fasta file for this assembly may be found. Server and path should be separated by a semi-colon.It should be directory and file optional: assemblyLocalPath is the path plus filename to the assembly genome fasta file that can be accessed from this program. This file is used to create am MD5 hash for the genome_file_data table.

Returns:

Wgs Key File

wGSKeyFile

@NotNull
public LoadHaplotypesFromGVCFPlugin wGSKeyFile(@NotNull
                                                        java.lang.String value)

Set Wgs Key File. Keyfile used to specify the inputs to the DB. Must have columns sample_name, files, type, chrPhased, genePhased, phasingConf and gvcfServerPath. Optionally you can have sample_description, assemblyServerPath, assemblyLocalPath. Ordering of the columns does not matter. sample_name is the name of the taxon you are uploading. files is a comma-separated list of file names(without path) providing the names of the GVCF files to be uploaded. If there are multiple files, gamete_ids will be assigned in order. type is the type of the files. To use this for this Plugin GVCF needs to be specified.chrPhased and genePhased must be either 'true' or 'false' and represent if the chromosome or the genes are phased or not phasingConf must be a number between 0.0 and 1.0 representing the confidence in the phasing. sample_description to provide a short description of the sample name to be uploaded. If this column is not specified an empty description will be used. optional: assemblyServerPath is an external server and path where the genome fasta file for this assembly may be found. Server and path should be separated by a semi-colon.It should be directory and file optional: assemblyLocalPath is the path plus filename to the assembly genome fasta file that can be accessed from this program. This file is used to create am MD5 hash for the genome_file_data table.

Parameters:

value - Wgs Key File

Returns:

this plugin

gVCFDirectory

@NotNull
public java.lang.String gVCFDirectory()

Directory holding all the gvcf files

Returns:

Gvcf Dir

gVCFDirectory

@NotNull
public LoadHaplotypesFromGVCFPlugin gVCFDirectory(@NotNull
                                                           java.lang.String value)

Set Gvcf Dir. Directory holding all the gvcf files

Parameters:

value - Gvcf Dir

Returns:

this plugin

reference

@NotNull
public java.lang.String reference()

Input Reference Fasta

Returns:

Ref

reference

@NotNull
public LoadHaplotypesFromGVCFPlugin reference(@NotNull
                                                       java.lang.String value)

Set Ref. Input Reference Fasta

Parameters:

value - Ref

Returns:

this plugin

bedFile

@NotNull
public java.lang.String bedFile()

File holding the Reference Range Information

Returns:

Bed File

bedFile

@NotNull
public LoadHaplotypesFromGVCFPlugin bedFile(@NotNull
                                                     java.lang.String value)

Set Bed File. File holding the Reference Range Information

Parameters:

value - Bed File

Returns:

this plugin

method

@NotNull
public java.lang.String method()

Method name for the haplotypes being uploaded.

Returns:

Method

method

@NotNull
public LoadHaplotypesFromGVCFPlugin method(@NotNull
                                                    java.lang.String value)

Set Method. Method name for the haplotypes being uploaded.

Parameters:

value - Method

Returns:

this plugin

methodDescription

@NotNull
public java.lang.String methodDescription()

Method description to be written if the method is new.

Returns:

Method Description

methodDescription

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

Set Method Description. Method description to be written if the method is new.

Parameters:

value - Method Description

Returns:

this plugin

numThreads

public int numThreads()

Number of threads used to upload

Returns:

Num Threads

numThreads

@NotNull
public LoadHaplotypesFromGVCFPlugin numThreads(int value)

Set Num Threads. Number of threads used to upload

Parameters:

value - Num Threads

Returns:

this plugin

maxDBUploadQueue

public int maxDBUploadQueue()

Number of Haplotype instances to stage per chromosome before a DB write is triggered. Lower this number if you are running into RAM issues. It will take longer to process, but should help balance the load.

Returns:

Max Num Haps Staged

maxDBUploadQueue

@NotNull
public LoadHaplotypesFromGVCFPlugin maxDBUploadQueue(int value)

Set Max Num Haps Staged. Number of Haplotype instances to stage per chromosome before a DB write is triggered. Lower this number if you are running into RAM issues. It will take longer to process, but should help balance the load.

Parameters:

value - Max Num Haps Staged

Returns:

this plugin

mergeRefBlocks

public boolean mergeRefBlocks()

Merge consecutive GVCF ReferenceBlocks together. If there is at least 1 bp between two gvcf refBlock records, the records will not be merged

Returns:

Merge Ref Blocks

mergeRefBlocks

@NotNull
public LoadHaplotypesFromGVCFPlugin mergeRefBlocks(boolean value)

Set Merge Ref Blocks. Merge consecutive GVCF ReferenceBlocks together. If there is at least 1 bp between two gvcf refBlock records, the records will not be merged

Parameters:

value - Merge Ref Blocks

Returns:

this plugin

queueSize

public int queueSize()

Size of Queue to pass information to the DB writing thread. Increase this number to have better thread utilization at the expense of RAM. If you are running into Java heap Space/RAM issues and cannot use a bigger machine, decrease this parameter.

Returns:

Queue Size

queueSize

@NotNull
public LoadHaplotypesFromGVCFPlugin queueSize(int value)

Set Queue Size. Size of Queue to pass information to the DB writing thread. Increase this number to have better thread utilization at the expense of RAM. If you are running into Java heap Space/RAM issues and cannot use a bigger machine, decrease this parameter.

Parameters:

value - Queue Size

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 LoadHaplotypesFromGVCFPlugin 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