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Simple implementation to retrieve relevant BAM files for each sample 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5152 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-02-01 00:03:03 +00:00
parent e74f28ad89
commit a89400b20c
1 changed files with 19 additions and 3 deletions
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22
scala/qscript/oneoffs/fromer/phaseSamples.scala
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@ -90,9 +90,25 @@ def bamsToTargets(samples: List[String], bamsIn: File): List[Target] = {
// these files // these files
def findBamsForSamples( samples: List[String], bams: List[File] ): List[File] = bams match { def findBamsForSamples( samples: List[String], bams: List[File] ): List[File] = bams match {
case x :: Nil => return bams case x :: Nil => return bams
case _ => case _ =>
// todo -- implement me return findBamsForSamplesHelper(samples, bams)
throw new RuntimeException("bam input lists not enabled") }
def findBamsForSamplesHelper( samples: List[String], bams: List[File] ): List[File] = bams match {
case Nil => Nil
case x :: y =>
val line: File = matchSamplesInSingleBam(x, samples)
val restOfList: List[File] = findBamsForSamplesHelper(samples, y)
if (line != null)
line :: restOfList
else
restOfList
}
// If the line (bam file name) contains ANY sample match, we use it:
def matchSamplesInSingleBam( line : File, samples: List[String] ) : File = samples match {
case Nil => null
case x :: y => if (line.getName().contains(x)) line else matchSamplesInSingleBam(line, y)
} }
// todo -- allow us to get the master list of samples from the VCF for convenience // todo -- allow us to get the master list of samples from the VCF for convenience