98 lines
2.5 KiB
Scala
Executable File
98 lines
2.5 KiB
Scala
Executable File
package org.broadinstitute.sting.queue
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import collection.mutable.ListBuffer
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import collection.JavaConversions._
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import org.broadinstitute.sting.queue.util.Logging
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import org.broadinstitute.sting.utils.text.XReadLines
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import java.io.{FileInputStream, File}
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import java.util.Properties
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class QArguments(args: Array[String]) {
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var useBsub = false
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var dryRun = false
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val scripts = new ListBuffer[String]
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var inputPaths = List.empty[File]
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var argMap = Map.empty[String, String]
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parseArgs(args)
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private def parseArgs(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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dryRun = true
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if (isFlagged(filtered, "-bsub"))
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useBsub = true
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for (arg <- getArgs(filtered, "-P"))
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addArg(arg)
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for (arg <- getArgs(filtered, "-I"))
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addFile(arg)
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for (arg <- getArgs(filtered, "-S"))
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scripts.append(arg)
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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 addArg(arg: String) = {
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var file = new File(arg)
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if (arg.contains("=") && !file.exists) {
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val tokens = arg.split("=", 2)
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argMap = argMap.updated(tokens(0), tokens(1))
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} else if (file.exists && arg.endsWith(".properties")) {
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var props = new Properties
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props.load(new FileInputStream(file))
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for ((name, value) <- props)
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argMap = argMap.updated(name, value)
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}
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}
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def addFile(arg: String): Unit = {
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var file = new File(arg)
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if (arg.endsWith(".list")) {
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new XReadLines(file).iterator.foreach(addFile(_))
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} else {
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inputPaths = inputPaths ::: List(file)
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}
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}
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}
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object QArguments {
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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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}
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