biolockj.module.seq

Class Gunzipper

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.seq.Gunzipper

All Implemented Interfaces:

BioModule, ScriptModule, SeqModule, Comparable<BioModule>

public class Gunzipper
extends SeqModuleImpl

This BioModule uses gzip to decompress input sequence files.

GUI Module Name

Decompress .gz Files

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	FUNCTION_GUNZIP Name of the bash function used to decompress gzipped files: "openZip"

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.ScriptModule

SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
Gunzipper()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Method returns a nested list of bash script lines to classify samples containing forward reads only.
List<String>	getWorkerScriptFunctions() This method generates the bash function: "openZip".

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, getSummary, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, checkDependencies, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getTempDir, init, toString, validateFileNameUnique

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getTempDir, init

Field Detail

FUNCTION_GUNZIP

protected static final String FUNCTION_GUNZIP

Name of the bash function used to decompress gzipped files: "openZip"

See Also:

Constant Field Values

Constructor Detail

Gunzipper

public Gunzipper()

Method Detail

buildScript

public List<List<String>> buildScript(List<File> files)
                               throws Exception

Description copied from interface: ScriptModule

Method returns a nested list of bash script lines to classify samples containing forward reads only. The inner list contains the bash script lines required to classify 1 sample.

Specified by:

buildScript in interface ScriptModule

Specified by:

buildScript in class ScriptModuleImpl

Parameters:

files - Files in the input directory that contain only forward reads

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate script lines

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

This method generates the bash function: "openZip".

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur