Handle Illumina 1.3-1.7 fastq as input to bwa mem via converstion with fastx_toolkit. Include conversion as part of fastq preparation of bgzip indexed files for parallel alignment. Fixes #190
Ensure clean retries when preparing bgzipped fastq input from BAM and fail on initial compression. Avoid retry within transactional directory
Avoid use of Python 2.7 specific subprocess.check_output. Fixes #192