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biopet.biopet
Commits
243fd59a
Commit
243fd59a
authored
Oct 10, 2014
by
bow
Browse files
Set default validation stringency to lenient in WipeReads
parent
634364dd
Changes
1
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala
View file @
243fd59a
...
...
@@ -165,6 +165,7 @@ object WipeReads extends MainCommand {
new
SAMFileReader
(
inBAM
,
inBAMIndex
)
else
{
val
sfr
=
new
SAMFileReader
(
inBAM
)
sfr
.
setValidationStringency
(
SAMFileReader
.
ValidationStringency
.
LENIENT
)
if
(!
sfr
.
hasIndex
)
throw
new
IllegalStateException
(
"Input BAM file must be indexed"
)
else
...
...
@@ -312,6 +313,7 @@ object WipeReads extends MainCommand {
.
setCreateIndex
(
writeIndex
)
.
setUseAsyncIo
(
async
)
val
templateBAM
=
new
SAMFileReader
(
inBAM
)
templateBAM
.
setValidationStringency
(
SAMFileReader
.
ValidationStringency
.
LENIENT
)
val
targetBAM
=
factory
.
makeBAMWriter
(
templateBAM
.
getFileHeader
,
true
,
outBAM
)
val
filteredBAM
=
if
(
filteredOutBAM
!=
null
)
...
...
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