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biopet.biopet
Commits
6f001daf
Commit
6f001daf
authored
May 04, 2016
by
Peter van 't Hof
Browse files
Added allele index to deps
parent
26fa9924
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
View file @
6f001daf
...
...
@@ -411,7 +411,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
if
(
bamOutput
!=
null
&&
!
org
.
broadinstitute
.
gatk
.
utils
.
io
.
IOUtils
.
isSpecialFile
(
bamOutput
))
if
(
generate_md5
)
bamOutputMD5
=
new
File
(
bamOutput
.
getPath
+
".md5"
)
alleles
.
foreach
(
VcfUtils
.
getVcfIndexFile
(
_
))
alleles
.
foreach
(
deps
:+=
VcfUtils
.
getVcfIndexFile
(
_
))
num_cpu_threads_per_data_thread
=
Some
(
getThreads
)
}
...
...
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