ensure we use fixed location for bwa throughout script
ensure we fail early on not finding bwa
Merge pull request #47 from dkj/devel

ensure we use consistent bwa throughout script
pb_align: check flagstats before AND after spatial_filter, fix for single-ended bam files, tidied code tag
pb_calibration: when checking for paired-end bam files include QC failed
predictor_pu.c: force N's to have quality 0 and set min quality for non N's to 1 cd bcl file where N <=> quality 0
parse_bam.c: update alignment parsing to handle indels at start/end of aligmnet and ambiguity codes in MD tag
corrected comment
Merge branch 'wtsi-npg/devel' into devel

Conflicts:
	bin/pb_align
Merge pull request #48 from srl147/devel

pb_align: check flagstats before AND after spatial_filter, fix for singl...
Merge pull request #49 from wtsi-npg/devel

Devel