Bowtie 1.2 breaks `emirge`

[andersgs]

Hello.

I know emirge has only been tested on versions 0.12* or so of bowtie. But, we had no issues running it up to version 1.1.2 of bowtie. A recent upgrade to bowtie 1.2, however, broke emirge.

The command generated at do_initial_mapping does not seem to work. We get an error saying the file does not appear to be a FASTQ file.

Running latest build of emirge (0.61.0), python 2.7.13, and latest versions of numpy, scipy, biopython, and pysam.

[cjfields]

Seeing the same here.