74 lines
1.7 KiB
Scala
Executable File
74 lines
1.7 KiB
Scala
Executable File
package org.broadinstitute.sting.queue
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import collection.mutable.ListBuffer
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import engine.Pipeline
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import org.broadinstitute.sting.queue.util.Logging
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object QArguments {
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val scripts = new ListBuffer[String]
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def parseArgs(args: Array[String]) {
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filterArgs(args)
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}
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/**
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* Pull out any args that are meant for QCommandLine
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*/
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private def filterArgs(args: Array[String]) = {
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var filtered = new ListBuffer[String]
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filtered.appendAll(args)
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if (isFlagged(filtered, "-debug"))
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Logging.enableDebug
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if (isFlagged(filtered, "-dry"))
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Pipeline.dryRun = true
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if (isFlagged(filtered, "-bsub"))
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Pipeline.useBsub = true
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for (arg <- getArgs(filtered, "-P"))
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Pipeline.addArg(arg)
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for (arg <- getArgs(filtered, "-I"))
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Pipeline.addFile(arg)
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for (arg <- getArgs(filtered, "-S"))
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scripts.append(arg)
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filtered
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}
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private def isFlagged(filtered: ListBuffer[String], search: String) = {
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var found = false
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var index = 0
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while (0 <= index && index < filtered.size) {
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index = filtered.indexOf(search)
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if (index >= 0) {
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found = true
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filtered.remove(index)
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}
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}
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found
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}
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private def getArgs(filtered: ListBuffer[String], search: String) = {
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var found = new ListBuffer[String]
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var index = 0
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while (0 <= index && index < filtered.size) {
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index = filtered.indexOf(search)
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if (index >= 0) {
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found.append(filtered(index+1))
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filtered.remove(index, 2)
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}
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}
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found
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}
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def strip(filtered: ListBuffer[String], search: String) = {
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var index = 0
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while (0 <= index && index < filtered.size) {
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index = filtered.indexOf(search)
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if (index >= 0) {
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filtered.remove(index, 2)
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}
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}
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}}
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