zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-07-13 13:00:55 -04:00
parent 74aa49e423 ff4e31c554
commit e2f2917bd2
1 changed files with 5 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
View File

@ -41,11 +41,11 @@ class RecalibrateBaseQualities extends QScript {
nContigs = getNumberOfContigs(input) nContigs = getNumberOfContigs(input)
val recalFile1: File = swapExt(input, ".bam", "recal1.csv") val recalFile1: File = swapExt(input, ".bam", ".recal1.csv")
val recalFile2: File = swapExt(input, ".bam", "recal2.csv") val recalFile2: File = swapExt(input, ".bam", ".recal2.csv")
val recalBam: File = swapExt(input, ".bam", "recal.bam") val recalBam: File = swapExt(input, ".bam", ".recal.bam")
val path1: String = "before" val path1: String = input + "before"
val path2: String = "after" val path2: String = input + "after"
add(cov(input, recalFile1), add(cov(input, recalFile1),
recal(input, recalFile1, recalBam), recal(input, recalFile1, recalBam),