net.maizegenetics.pangenome.processAssemblyGenomes

Class RampSeqContigToGenomeIntervalPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener

public class RampSeqContigToGenomeIntervalPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

NOTE: this method created to aid Dan Ilut. It is not official part of Assembly pipeline This method takes a sorted/indexed BAM File or a SAM file. It uses htsjdk to read the BAM file and find locations of the assembly contigs in the reference genome. These locations are then mapped to genome_intervals (anchors or inter-anchors) in the db.. Genome Interval identification is based on the mid-point of the reference range where the contig maps. Use htsjdk to get the start/end of alignment from SamRecord, find the midpoint of this alignment, search the ReferenceRanges from the db to find the range (ie genome interval) where this read falls. Output: A tab delimited file with the headings: ContigNam GenomeIntervalRange GenomeIntervalId IsAnchor The file name is the BAM/SAM file name minus the extension, plus "_intervalMapping.txt", written to the specified user directory. For example: outputDir = /workdir/lcj34/danOutput/ BAM file = /workdir/lcj34/bamFiles/w22B73Asm10.bam output File from this plugin: /workdir/lcj34/danOutput/w22B73Asm10_intervalMapping.txt

Author:

lcj34

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
RampSeqContigToGenomeIntervalPlugin()
RampSeqContigToGenomeIntervalPlugin(Frame parentFrame)
RampSeqContigToGenomeIntervalPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	contigBAM() Name of contig BAM file to process
RampSeqContigToGenomeIntervalPlugin	contigBAM(String value) Set Contig File.
String	databaseName() Database name
RampSeqContigToGenomeIntervalPlugin	databaseName(String value) Set Database Name.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	hostname() Hostname where database resides
RampSeqContigToGenomeIntervalPlugin	hostname(String value) Set Hostname.
static void	main(String[] args)
String	outputDir() Output Directory
RampSeqContigToGenomeIntervalPlugin	outputDir(String value) Set Output Directory.
String	password() Password for database
RampSeqContigToGenomeIntervalPlugin	password(String value) Set Password.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	userid() Userid for database
RampSeqContigToGenomeIntervalPlugin	userid(String value) Set Userid.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

RampSeqContigToGenomeIntervalPlugin

public RampSeqContigToGenomeIntervalPlugin()

RampSeqContigToGenomeIntervalPlugin

public RampSeqContigToGenomeIntervalPlugin(Frame parentFrame)

RampSeqContigToGenomeIntervalPlugin

public RampSeqContigToGenomeIntervalPlugin(Frame parentFrame,
                                           boolean isInteractive)

Method Detail

main

public static void main(String[] args)

Parameters:

args -

processData

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

Specified by:

processData in interface net.maizegenetics.plugindef.Plugin

Overrides:

processData in class net.maizegenetics.plugindef.AbstractPlugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

hostname

public String hostname()

Hostname where database resides

Returns:

Hostname

hostname

public RampSeqContigToGenomeIntervalPlugin hostname(String value)

Set Hostname. Hostname where database resides

Parameters:

value - Hostname

Returns:

this plugin

userid

public String userid()

Userid for database

Returns:

Userid

userid

public RampSeqContigToGenomeIntervalPlugin userid(String value)

Set Userid. Userid for database

Parameters:

value - Userid

Returns:

this plugin

password

public String password()

Password for database

Returns:

Password

password

public RampSeqContigToGenomeIntervalPlugin password(String value)

Set Password. Password for database

Parameters:

value - Password

Returns:

this plugin

databaseName

public String databaseName()

Database name

Returns:

Database Name

databaseName

public RampSeqContigToGenomeIntervalPlugin databaseName(String value)

Set Database Name. Database name

Parameters:

value - Database Name

Returns:

this plugin

contigBAM

public String contigBAM()

Name of contig BAM file to process

Returns:

Contig File

contigBAM

public RampSeqContigToGenomeIntervalPlugin contigBAM(String value)

Set Contig File. Name of contig fasta file to process

Parameters:

value - Contig File

Returns:

this plugin

outputDir

public String outputDir()

Output Directory

Returns:

Output Directory

outputDir

public RampSeqContigToGenomeIntervalPlugin outputDir(String value)

Set Output Directory. Output Directory

Parameters:

value - Output Directory

Returns:

this plugin