pb_align: check flagstats before AND after spatial_filter, fix for singl...

...e-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