biolockj.module.implicit

Class RegisterNumReads

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.implicit.RegisterNumReads

All Implemented Interfaces:

BioModule, JavaModule, ReadCounter, ScriptModule, SeqModule, Comparable<BioModule>

public class RegisterNumReads
extends JavaModuleImpl
implements SeqModule, ReadCounter

This BioModule parses sequence file to count the number of reads per sample. The data is stored in a new column Num_Reads. If no metadata file exists, it is created with 2 columns: SampleID and Num_Reads.

GUI Module Name

Register Number of Reads

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	NUM_READS Metadata column name for column that holds number of reads per sample: "Num_Reads"

Fields inherited from class biolockj.module.JavaModuleImpl

BLJ_OPTIONS

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.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
RegisterNumReads()

Method Summary

Modifier and Type	Method and Description
static Set<String>	getDepricatedReadFields() Getter for depricatedReadFields
static String	getNumReadFieldName() Getter for numReadFieldName
List<File>	getSeqFiles(Collection<File> files) Return only sequence files for sample IDs found in the metadata file. If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.
String	getSummary() Produce summary message with min, max, mean, and median number of reads.
void	runModule() Register number of reads for each sample by parsing each file and counting number of lines.
static void	setNumReadFieldName(String name) When a module modifies the number of reads, the new counts must replace the old count fields.

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, isValidInputModule, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface biolockj.module.ScriptModule

buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version

Field Detail

NUM_READS

protected static final String NUM_READS

Metadata column name for column that holds number of reads per sample: "Num_Reads"

See Also:

Constant Field Values

Constructor Detail

RegisterNumReads

public RegisterNumReads()

Method Detail

getSeqFiles

public List<File> getSeqFiles(Collection<File> files)
                       throws SequnceFormatException

Description copied from interface: SeqModule

Return only sequence files for sample IDs found in the metadata file.
If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.

Specified by:

getSeqFiles in interface SeqModule

Parameters:

files - Module input files

Returns:

Module sequence files

Throws:

SequnceFormatException - If Config."metadata.required" = "Y" but sequence files found that do not have a corresponding record in the metadata file or if invalid metadata prevents parsing SEQ files.

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 ScriptModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

runModule

public void runModule()
               throws Exception

Register number of reads for each sample by parsing each file and counting number of lines. Add "Num_Reads" column to metadata and refresh the cache.

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

getDepricatedReadFields

public static Set<String> getDepricatedReadFields()

Getter for depricatedReadFields

Returns:

depricatedReadFields

getNumReadFieldName

public static String getNumReadFieldName()

Getter for numReadFieldName

Returns:

numReadFieldName

setNumReadFieldName

public static void setNumReadFieldName(String name)
                                throws Exception

When a module modifies the number of reads, the new counts must replace the old count fields.

Parameters:

name - Name of new number of reads metadata field

Throws:

Exception - if null value passed