Commit 9e21462b authored by Peter van 't Hof's avatar Peter van 't Hof

Remove old report

parent 7bd7b5a9
......@@ -57,14 +57,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
case f: BiopetCommandLineFunctionTrait => f.afterGraph
case _ =>
}
val configReport = Config.global.getReport
val configReportFile = new File(outputDir + qSettings.runName + ".configreport.txt")
configReportFile.getParentFile.mkdir
val writer = new PrintWriter(configReportFile)
writer.write(configReport)
writer.close()
Config.global.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
for (line <- configReport.split("\n")) logger.debug(line)
}
def add(functions: QFunction*) // Gets implemeted at org.broadinstitute.sting.queue.QScript
......
......@@ -140,40 +140,6 @@ class Config(var map: Map[String, Any]) extends Logging {
} else throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
}
//TODO: New version of report is needed
/**
* Makes report for all used values
* @deprecated
* @return Config report
*/
def getReport: String = {
val output: StringBuilder = new StringBuilder
output.append("Config report, sorted on module:\n")
var modules: Map[String, StringBuilder] = Map()
for ((key, value) <- foundCache) {
val module = key.module
if (!modules.contains(module)) modules += (module -> new StringBuilder)
modules(module).append("Found: " + value.toString + "\n")
}
for ((key, value) <- defaultCache) {
val module = key.module
if (!modules.contains(module)) modules += (module -> new StringBuilder)
modules(module).append("Default used: " + value.toString + "\n")
}
for (value <- notFoundCache) {
val module = value.module
if (!modules.contains(module)) modules += (module -> new StringBuilder)
if (!defaultCache.contains(value)) modules(module).append("Not Found: " + value.toString + "\n")
}
for ((key, value) <- modules) {
output.append("Config options for module: " + key + "\n")
output.append(value.toString)
output.append("\n")
}
return output.toString
}
def writeReport(id: String, directory: String): Unit = {
def convertIndexValuesToMap(input: List[(ConfigValueIndex, Any)], forceFreeVar: Option[Boolean] = None): Map[String, Any] = {
......
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