From 5044b1d53601ca153db055ddaa564dac86a23d9f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 5 Apr 2016 16:19:26 +0200
Subject: [PATCH] Added more args
---
.../lumc/sasc/biopet/extensions/Snptest.scala | 45 ++++++++++++++++++-
1 file changed, 43 insertions(+), 2 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
index 9d43e04e7..d1948f5f1 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
@@ -35,8 +35,31 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
var totalProbLimit: Option[Double] = config("total_prob_limit")
var tableName: Option[String] = config("table_name")
var useLongColumnNamingScheme: Boolean = config("use_long_column_naming_scheme", default = false)
+
+ var excludeSamples: List[String] = config("exclude_samples", default = Nil)
+
+ @Input(required = false)
+ val excludeSnp: Option[File] = config("exclude_snp")
+
+ var missThresh: Option[Double] = config("miss_thresh")
+ var baselinePhenotype: Option[String] = config("baseline_phenotype")
+ var bayesian: List[String] = config("bayesian", default = Nil)
+ var callThresh: Option[Double] = config("call_thresh")
+ var frequentist: List[String] = config("frequentist", default = Nil)
+ var fullParameterEstimates: Boolean = config("full_parameter_estimates", default = false)
+ var method: Option[String] = config("method")
+ var pheno: Option[String] = config("pheno")
var summaryStatsOnly: Boolean = config("summary_stats_only", default = false)
+ var covAll: Boolean = config("cov_all", default = false)
+ var covAllContinuous: Boolean = config("cov_all_continuous", default = false)
+ var covAllDiscrete: Boolean = config("cov_all_discrete", default = false)
+ var covNames: List[String] = config("cov_names", default = Nil)
+ var sexColumn: Option[String] = config("sex_column")
+ var stratifyOn: Option[String] = config("stratify_on")
+
+ var conditionOn: List[String] = config("condition_on")
+
executable = config("exe", default = "snptest")
def versionCommand: String = executable + " -help"
@@ -48,7 +71,8 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
}
def multiArg(argName: String, values: Iterable[Any]): String = {
- required(argName) + values.map(required(_)).mkString
+ if (values.nonEmpty) required(argName) + values.map(required(_)).mkString
+ else ""
}
def cmdLine: String = {
@@ -66,7 +90,24 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
optional("-odb", outputDatabaseFile) +
optional("-table_name", tableName) +
conditional(useLongColumnNamingScheme, "-use_long_column_naming_scheme") +
- conditional(summaryStatsOnly, "-summary_stats_only")
+ multiArg("-exclude_samples", excludeSamples) +
+ optional("-exclude_snp", excludeSnp) +
+ optional("-miss_thresh", missThresh) +
+ optional("-baseline_phenotype", baselinePhenotype) +
+ multiArg("-bayesian", bayesian) +
+ optional("-call_thresh", callThresh) +
+ multiArg("-frequentist", frequentist) +
+ conditional(fullParameterEstimates, "-full_parameter_estimates") +
+ optional("-method", method) +
+ optional("-pheno", pheno)
+ conditional(summaryStatsOnly, "-summary_stats_only") +
+ conditional(covAll, "-cov_all") +
+ conditional(covAllContinuous, "-cov_all_continuous") +
+ conditional(covAllDiscrete, "-cov_all_discrete") +
+ multiArg("-cov_names", covNames) +
+ optional("-sex_column", sexColumn) +
+ optional("-stratify_on", stratifyOn) +
+ multiArg("-condition_on", conditionOn)
}
}
--
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