Commit cb1f06d1 authored by bow's avatar bow
Browse files

Allow for .bam.bai or .bai extension

parent 04599e18
......@@ -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
|
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment