From 674e3168bada9e6e0220af32b241f648aa7179db Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Tue, 19 Jan 2016 18:10:46 +0100
Subject: [PATCH] Style refactor of PindelCaller wrapper
---
.../extensions/pindel/PindelCaller.scala | 125 +++++++++---------
1 file changed, 64 insertions(+), 61 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
index 0ccb2468b..f0bc396a3 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala
@@ -34,48 +34,49 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
override def defaultCoreMemory = 4.0
override def defaultThreads = 4
- override def versionRegex = """Pindel version:? (.*)""".r
+ def versionRegex = """Pindel version:? (.*)""".r
override def versionExitcode = List(1)
- override def versionCommand = executable
+ def versionCommand = executable
/**
* Required parameters
*/
+ @Input
var reference: File = referenceFasta
@Input(doc = "Input specification for Pindel to use")
var input: File = _
@Argument(doc = "The pindel configuration file", required = false)
- var pindel_file: Option[File] = None
+ var pindelFile: Option[File] = None
@Argument(doc = "Configuration file with: bam-location/insert size/name", required = false)
- var config_file: Option[File] = None
+ var configFile: Option[File] = None
@Argument(doc = "Work directory")
- var output_prefix: File = _
+ var outputPrefix: File = _
@Output(doc = "Output file of pindel, pointing to the DEL file")
- var output_file: File = _
+ var outputFile: File = _
var RP: Option[Int] = config("RP")
- var min_distance_to_the_end: Option[Int] = config("min_distance_to_the_end")
+ var minDistanceToTheEnd: Option[Int] = config("min_distance_to_the_end")
// var threads
- var max_range_index: Option[Int] = config("max_range_index")
- var window_size: Option[Int] = config("window_size")
- var sequencing_error_rate: Option[Float] = config("sequencing_error_rate")
+ var maxRangeIndex: Option[Int] = config("max_range_index")
+ var windowSize: Option[Int] = config("window_size")
+ var sequencingErrorRate: Option[Float] = config("sequencing_error_rate")
var sensitivity: Option[Float] = config("sensitivity")
- var maximum_allowed_mismatch_rate: Option[Float] = config("maximum_allowed_mismatch_rate")
+ var maximumAllowedMismatchRate: Option[Float] = config("maximum_allowed_mismatch_rate")
var nm: Option[Int] = config("nm")
- var report_inversions: Boolean = config("report_inversions", default = false)
- var report_duplications: Boolean = config("report_duplications", default = false)
- var report_long_insertions: Boolean = config("report_long_insertions", default = false)
- var report_breakpoints: Boolean = config("report_breakpoints", default = false)
- var report_close_mapped_reads: Boolean = config("report_close_mapped_reads", default = false)
- var report_only_close_mapped_reads: Boolean = config("report_only_close_mapped_reads", default = false)
- var report_interchromosomal_events: Boolean = config("report_interchromosomal_events", default = false)
+ var reportInversions: Boolean = config("report_inversions", default = false)
+ var reportDuplications: Boolean = config("report_duplications", default = false)
+ var reportLongInsertions: Boolean = config("report_long_insertions", default = false)
+ var reportBreakpoints: Boolean = config("report_breakpoints", default = false)
+ var reportCloseMappedReads: Boolean = config("report_close_mapped_reads", default = false)
+ var reportOnlyCloseMappedReads: Boolean = config("report_only_close_mapped_reads", default = false)
+ var reportInterchromosomalEvents: Boolean = config("report_interchromosomal_events", default = false)
var IndelCorrection: Boolean = config("IndelCorrection", default = false)
var NormalSamples: Boolean = config("NormalSamples", default = false)
@@ -84,21 +85,21 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
var include: Option[File] = config("include")
var exclude: Option[File] = config("exclude")
- var additional_mismatch: Option[Int] = config("additional_mismatch")
- var min_perfect_match_around_BP: Option[Int] = config("min_perfect_match_around_BP")
- var min_inversion_size: Option[Int] = config("min_inversion_size")
- var min_num_matched_bases: Option[Int] = config("min_num_matched_bases")
- var balance_cutoff: Option[Int] = config("balance_cutoff")
- var anchor_quality: Option[Int] = config("anchor_quality")
- var minimum_support_for_event: Option[Int] = config("minimum_support_for_event")
- var input_SV_Calls_for_assembly: Option[File] = config("input_SV_Calls_for_assembly")
+ var additionalMismatch: Option[Int] = config("additional_mismatch")
+ var minPerfectMatchAroundBP: Option[Int] = config("min_perfect_match_around_BP")
+ var minInversionSize: Option[Int] = config("min_inversion_size")
+ var minNumMatchedBases: Option[Int] = config("min_num_matched_bases")
+ var balanceCutoff: Option[Int] = config("balance_cutoff")
+ var anchorQuality: Option[Int] = config("anchor_quality")
+ var minimumSupportForEvent: Option[Int] = config("minimum_support_for_event")
+ var inputSVCallsForAssembly: Option[File] = config("input_SV_Calls_for_assembly")
var genotyping: Boolean = config("genotyping", default = false)
- var output_of_breakdancer_events: Option[File] = config("output_of_breakdancer_events")
- var name_of_logfile: Option[File] = config("name_of_logfile")
+ var outputOfBreakdancerEvents: Option[File] = config("output_of_breakdancer_events")
+ var nameOfLogfile: Option[File] = config("name_of_logfile")
- var Ploidy: Option[File] = config("ploidy")
- var detect_DD: Boolean = config("detect_DD", default = false)
+ var ploidy: Option[File] = config("ploidy")
+ var detectDD: Boolean = config("detect_DD", default = false)
var MAX_DD_BREAKPOINT_DISTANCE: Option[Int] = config("MAX_DD_BREAKPOINT_DISTANCE")
var MAX_DISTANCE_CLUSTER_READS: Option[Int] = config("MAX_DISTANCE_CLUSTER_READS")
@@ -108,9 +109,11 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
var DD_REPORT_DUPLICATION_READS: Option[Int] = config("DD_REPORT_DUPLICATION_READS")
override def beforeGraph: Unit = {
+ if (reference == null) reference = referenceFasta()
+
// we should check whether the `pindel-config-file` is set or the `config-file` for the bam-list
// at least one of them should be set.
- (pindel_file, config_file) match {
+ (pindelFile, configFile) match {
case (None, None) => Logging.addError("No pindel config is given")
case (Some(a), Some(b)) => Logging.addError(s"Please specify either a pindel config or bam-config. Not both for Pindel: $a or $b")
case (Some(a), None) => {
@@ -125,48 +128,48 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
// set the output file, the DELetion call is always made
// TODO: add more outputs for the LI, SI, INV etc...
- output_file = new File(output_prefix + File.separator, "sample_D")
+ outputFile = new File(outputPrefix + File.separator, "sample_D")
}
def cmdLine = required(executable) +
required("--fasta ", reference) +
- optional("--pindel-config-file", pindel_file) +
- optional("--config-file", config_file) +
- required("--output-prefix ", new File(output_prefix + File.separator, "sample")) +
+ optional("--pindel-config-file", pindelFile) +
+ optional("--config-file", configFile) +
+ required("--output-prefix ", new File(outputPrefix + File.separator, "sample")) +
optional("--RP", RP) +
- optional("--min_distance_to_the_end", min_distance_to_the_end) +
+ optional("--min_distance_to_the_end", minDistanceToTheEnd) +
optional("--number_of_threads", threads) +
- optional("--max_range_index", max_range_index) +
- optional("--windows_size", window_size) +
- optional("--sequencing_error_rate", sequencing_error_rate) +
+ optional("--max_range_index", maxRangeIndex) +
+ optional("--windows_size", windowSize) +
+ optional("--sequencing_error_rate", sequencingErrorRate) +
optional("--sensitivity", sensitivity) +
- optional("--maximum_allowed_mismatch_rate", maximum_allowed_mismatch_rate) +
+ optional("--maximum_allowed_mismatch_rate", maximumAllowedMismatchRate) +
optional("--NM", nm) +
- conditional(report_inversions, "--report_inversions") +
- conditional(report_duplications, "--report_duplications") +
- conditional(report_long_insertions, "--report_long_insertions") +
- conditional(report_breakpoints, "--report_breakpoints") +
- conditional(report_close_mapped_reads, "--report_close_mapped_reads") +
- conditional(report_only_close_mapped_reads, "--report_only_close_mapped_reads") +
- conditional(report_interchromosomal_events, "--report_interchromosomal_events") +
+ conditional(reportInversions, "--report_inversions") +
+ conditional(reportDuplications, "--report_duplications") +
+ conditional(reportLongInsertions, "--report_long_insertions") +
+ conditional(reportBreakpoints, "--report_breakpoints") +
+ conditional(reportCloseMappedReads, "--report_close_mapped_reads") +
+ conditional(reportOnlyCloseMappedReads, "--report_only_close_mapped_reads") +
+ conditional(reportInterchromosomalEvents, "--report_interchromosomal_events") +
conditional(IndelCorrection, "--IndelCorrection") +
conditional(NormalSamples, "--NormalSamples") +
optional("--breakdancer", breakdancer) +
optional("--include", include) +
optional("--exclude", exclude) +
- optional("--additional_mismatch", additional_mismatch) +
- optional("--min_perfect_match_around_BP", min_perfect_match_around_BP) +
- optional("--min_inversion_size", min_inversion_size) +
- optional("--min_num_matched_bases", min_num_matched_bases) +
- optional("--balance_cutoff", balance_cutoff) +
- optional("--anchor_quality", anchor_quality) +
- optional("--minimum_support_for_event", minimum_support_for_event) +
- optional("--input_SV_Calls_for_assembly", input_SV_Calls_for_assembly) +
+ optional("--additional_mismatch", additionalMismatch) +
+ optional("--min_perfect_match_around_BP", minPerfectMatchAroundBP) +
+ optional("--min_inversion_size", minInversionSize) +
+ optional("--min_num_matched_bases", minNumMatchedBases) +
+ optional("--balance_cutoff", balanceCutoff) +
+ optional("--anchor_quality", anchorQuality) +
+ optional("--minimum_support_for_event", minimumSupportForEvent) +
+ optional("--input_SV_Calls_for_assembly", inputSVCallsForAssembly) +
conditional(genotyping, "-g") +
- optional("--output_of_breakdancer_events", output_of_breakdancer_events) +
- optional("--name_of_logfile", name_of_logfile) +
- optional("--Ploidy", Ploidy) +
- conditional(detect_DD, "detect_DD") +
+ optional("--output_of_breakdancer_events", outputOfBreakdancerEvents) +
+ optional("--name_of_logfile", nameOfLogfile) +
+ optional("--Ploidy", ploidy) +
+ conditional(detectDD, "detect_DD") +
optional("--MAX_DD_BREAKPOINT_DISTANCE", MAX_DD_BREAKPOINT_DISTANCE) +
optional("--MAX_DISTANCE_CLUSTER_READS", MAX_DISTANCE_CLUSTER_READS) +
optional("--MIN_DD_CLUSTER_SIZE", MIN_DD_CLUSTER_SIZE) +
@@ -178,8 +181,8 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
object PindelCaller {
def apply(root: Configurable, configFile: File, outputDir: File): PindelCaller = {
val caller = new PindelCaller(root)
- caller.config_file = Some(configFile)
- caller.output_prefix = outputDir
+ caller.configFile = Some(configFile)
+ caller.outputPrefix = outputDir
caller
}
}
--
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