Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
cb1f06d1
Commit
cb1f06d1
authored
Oct 05, 2014
by
bow
Browse files
Allow for .bam.bai or .bai extension
parent
04599e18
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala
View file @
cb1f06d1
...
...
@@ -241,7 +241,7 @@ object WipeReads {
def
checkInputBAM
(
inBAM
:
File
)
:
File
=
{
// input BAM must have a .bam.bai index
if
(
new
File
(
inBAM
.
getPath
+
".bai"
).
exists
)
if
(
new
File
(
inBAM
.
getPath
+
".bai"
).
exists
||
new
File
(
inBAM
.
getPath
+
".bam.bai"
).
exists
)
checkInputFile
(
inBAM
)
else
throw
new
IOException
(
"Index for input BAM file "
+
inBAM
.
getPath
+
" not found"
)
...
...
@@ -264,7 +264,7 @@ object WipeReads {
|WipeReads - Tool for reads removal from an indexed BAM file.
|
|positional arguments:
| -I,--inputBAM Input BAM file, must be indexed with '.bam.bai' extension
| -I,--inputBAM Input BAM file, must be indexed with '.bam.bai'
or 'bai'
extension
| -l,--targetRegions Input BED file
| -o,--outputBAM Output BAM file
|
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment