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 { ...@@ -241,7 +241,7 @@ object WipeReads {
def checkInputBAM(inBAM: File): File = { def checkInputBAM(inBAM: File): File = {
// input BAM must have a .bam.bai index // 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) checkInputFile(inBAM)
else else
throw new IOException("Index for input BAM file " + inBAM.getPath + " not found") throw new IOException("Index for input BAM file " + inBAM.getPath + " not found")
...@@ -264,7 +264,7 @@ object WipeReads { ...@@ -264,7 +264,7 @@ object WipeReads {
|WipeReads - Tool for reads removal from an indexed BAM file. |WipeReads - Tool for reads removal from an indexed BAM file.
| |
|positional arguments: |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 | -l,--targetRegions Input BED file
| -o,--outputBAM Output BAM file | -o,--outputBAM Output BAM file
| |
......
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