Test update (#38)

* add 1.96 version to picard calls

* add set -o pipefail to bwa call per jaeyoung bug ticket, update version

Author: lordzappo

cmo/_version.py

@@ -2,4 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-__version__ = '1.4.3'
+__version__ = '1.4.4'

cmo/bwa.py

@@ -56,7 +56,7 @@ def mem(self, fasta, fastq1, fastq2, output, args_dict=None, no_bam=False):
         if no_bam: 
             cmd = cmd + [">", output]
         else:
-            cmd = cmd + ["|", self.samtools_cmd, "view -bh - ", ">", output]
+            cmd = ["set -o pipefail;"] + cmd + ["|", self.samtools_cmd, "view -bh - ", ">", output]
         return " ".join(cmd)
     def sampe(self, fasta, sai1, sai2, fq1, fq2, output_bam, args_dict=None, no_bam=False):
         cmd = [self.bwa_cmd, "sampe"]