raphael-group/THetA — pull request #4 by etal (2014-09-29 18:26:15+00:00)
Title: Allow paths/filenames with spaces when calling samtools

In createTHetAExomeInput.py, quote the filename arguments inside each call to os.system to prevent the shell from parsing the space-containing argument as multiple tokens (i.e. garbage).

Alternative solutions not attempted here:
1. use subprocess & avoid using the shell altogether; or
2. use pysam & avoid creating the pileup files on disk.

Also fixed a typo.