biolockj.module.seq

Class PearMergeReads

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.seq.PearMergeReads

All Implemented Interfaces:

BioModule, ScriptModule, SeqModule, Comparable<BioModule>

public class PearMergeReads
extends SeqModuleImpl

This BioModule will merge forward and reverse fastq files using PEAR.
For more informations, see the online PEAR manual: https://sco.h-its.org/exelixis/web/software/pear/doc.html

GUI Module Name

Merge Reads with PEAR

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	EXE_PEAR Config property "exe.pear" defines the command line PEAR executable
protected static String	EXE_PEAR_PARAMS Config property "exe.pearParams" is used to set the PEAR executable runtime parameters
protected static String	FUNCTION_PEAR_MERGE Name of the bash function that merges files with PEAR: "mergeReads"
static String	NUM_MERGED_READS Metadata column name for column that holds number of reads per sample after merging: "Num_Merged_Reads"

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
PearMergeReads()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Build the script lines for each sample as a nested list.
void	checkDependencies() Validate module dependencies Verify input files are in fastq format Verify matching paired reads are found Validate required Config.EXE_PEAR property If running a restarted pipeline that already merged reads, set paired indicator to false
void	cleanUp() Set Config."internal.pairedReads" = "N" and register number of reads.
String	getSummary() Produce summary message with min, max, mean, and median number of reads.
List<String>	getWorkerScriptFunctions() This method generates the required bash functions used by the worker scripts: "mergeReads"

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, 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

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

Field Detail

NUM_MERGED_READS

public static final String NUM_MERGED_READS

Metadata column name for column that holds number of reads per sample after merging: "Num_Merged_Reads"

See Also:

Constant Field Values

EXE_PEAR

protected static final String EXE_PEAR

Config property "exe.pear" defines the command line PEAR executable

See Also:

Constant Field Values

EXE_PEAR_PARAMS

protected static final String EXE_PEAR_PARAMS

Config property "exe.pearParams" is used to set the PEAR executable runtime parameters

See Also:

Constant Field Values

FUNCTION_PEAR_MERGE

protected static final String FUNCTION_PEAR_MERGE

Name of the bash function that merges files with PEAR: "mergeReads"

See Also:

Constant Field Values

Constructor Detail

PearMergeReads

public PearMergeReads()

Method Detail

buildScript

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

Build the script lines for each sample as a nested list. PAIR program will be called once for each pair of files to output a single merged read.

Specified by:

buildScript in interface ScriptModule

Specified by:

buildScript in class ScriptModuleImpl

Parameters:

files - List of module input files

Returns:

List of nested bash script lines.

Throws:

Exception - if error occurs generating bash script lines

checkDependencies

public void checkDependencies()
                       throws Exception

Validate module dependencies

1. Verify input files are in fastq format
2. Verify matching paired reads are found
3. Validate required Config.EXE_PEAR property
4. If running a restarted pipeline that already merged reads, set paired indicator to false

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

cleanUp

public void cleanUp()
             throws Exception

Set Config."internal.pairedReads" = "N" and register number of reads.

Specified by:

cleanUp in interface BioModule

Overrides:

cleanUp in class BioModuleImpl

Throws:

Exception - thrown if any runtime error occurs

getSummary

public String getSummary()
                  throws Exception

Produce summary message with min, max, mean, and median number of reads.

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class SeqModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

This method generates the required bash functions used by the worker scripts: "mergeReads"

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur