Merge branch 'wtsi-npg-master' into devel
Merge remote branch 'js10-github/master' into devel
Merge remote branch 'js10-github/master' into devel
Merge branch 'devel' of github.com:wtsi-npg/pb_calibration into devel
merge follwoing conflict resolution
merge following conflict resolution
fix incorrect comment regarding return value of makeSurvTable
Merge pull request #42 from dkj/devel

Fix dodgy merge resolution
remove vestigial pread_bytes - has already been refactored into shared/cif.c
Merge pull request #43 from dkj/devel

Comment fix and vestigial code removal
moved flagstat after spatial_filter
fixed typo
Merge pull request #45 from srl147/devel

moved flagstat after spatial_filter and check for properly paired count rather than pairs aligned
Merge pull request #46 from wtsi-npg/devel

prep for release
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