Position problem of -b0 option on Mac OS X

[zyxue]

A strange error, the following command works on Linux but not on Mac OS X with bwa-0.7.9a.

bwa aln ref.fasta -b0 se.bam > sai

The following command works on both Linux and Mac OS X

bwa aln -b0 ref.fasta se.bam > sai

Any idea why this is the case? I am trying to run RNA-SeQC_v1.1.7.jar on Mac OS X, which constructs bwa command in the first pattern, and it produces the following error:

[bwa_seq_open] fail to open file '-b0' : No such file or directory

So for some reason, bwa aln consider -b0 to be an input file instead of a option when it's positioned after the ref.fasta. Anyway to get around this? Could it be due to any compilation problem, I simply used make on Mac OS X to compile bwa.

Thanks!

[LeightonP]

Command-line options are processed by different libraries on OSX and your Linux distro. The OSX libraries are more particular about option (things that begin with a hyphen, e.g. -b0) placement.

You'll find the same behaviour with tools like 'ls'.