public class RegisterNumReads extends JavaModuleImpl implements SeqModule, ReadCounter
Modifier and Type | Field and Description |
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protected static String |
NUM_READS
Metadata column name for column that holds number of reads per sample: "Num_Reads"
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BLJ_OPTIONS
GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT
LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR
Constructor and Description |
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RegisterNumReads() |
Modifier and Type | Method and Description |
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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.
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buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, isValidInputModule, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD
buildScriptForPairedReads, checkDependencies, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts, isValidProp
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
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions
checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version
protected static final String NUM_READS
public List<File> getSeqFiles(Collection<File> files) throws SequnceFormatException
SeqModule
Config
."metadata.required" = "Y", an
error is thrown to list the files that cannot be matched to a metadata row.getSeqFiles
in interface SeqModule
files
- Module input filesSequnceFormatException
- 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.public String getSummary() throws Exception
getSummary
in interface BioModule
getSummary
in class ScriptModuleImpl
Exception
- if any error occurspublic void runModule() throws Exception
runModule
in interface JavaModule
runModule
in class JavaModuleImpl
Exception
- thrown if any runtime error occurspublic static Set<String> getDepricatedReadFields()
public static String getNumReadFieldName()