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better progress report for the DPP

This commit is contained in:
Mauricio Carneiro 2011-07-18 23:39:47 -04:00
parent 2b465ab43b
commit 7688bda1a6
1 changed files with 10 additions and 3 deletions
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13
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -138,13 +138,22 @@ class DataProcessingPipeline extends QScript {
} }
} }
println("\n\n*** INPUT FILES ***\n")
// Creating one file for each sample in the dataset // Creating one file for each sample in the dataset
val sampleBamFiles = scala.collection.mutable.Map.empty[String, File] val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
for ((sample, flist) <- sampleTable) { for ((sample, flist) <- sampleTable) {
println(sample + ":")
for (f <- flist)
println (f)
println()
val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".bam") val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".bam")
sampleBamFiles(sample) = sampleFileName sampleBamFiles(sample) = sampleFileName
add(joinBams(flist, sampleFileName)) add(joinBams(flist, sampleFileName))
} }
println("*** INPUT FILES ***\n\n")
return sampleBamFiles.toMap return sampleBamFiles.toMap
} }
@ -211,9 +220,6 @@ class DataProcessingPipeline extends QScript {
// Generate a BAM file per sample joining all per lane files if necessary // Generate a BAM file per sample joining all per lane files if necessary
val sampleBamFiles: Map[String, File] = createSampleFiles(bams, realignedBams) val sampleBamFiles: Map[String, File] = createSampleFiles(bams, realignedBams)
println("nContigs: " + nContigs)
// Final output list of processed bam files // Final output list of processed bam files
var cohortList: List[File] = List() var cohortList: List[File] = List()
@ -221,6 +227,7 @@ class DataProcessingPipeline extends QScript {
println("\nFound the following samples: ") println("\nFound the following samples: ")
for ((sample, file) <- sampleBamFiles) for ((sample, file) <- sampleBamFiles)
println("\t" + sample + " -> " + file) println("\t" + sample + " -> " + file)
println("\n")
// If this is a 'knowns only' indel realignment run, do it only once for all samples. // If this is a 'knowns only' indel realignment run, do it only once for all samples.
val globalIntervals = new File(outputDir + projectName + ".intervals") val globalIntervals = new File(outputDir + projectName + ".intervals")