New -p switch for increased sensititivy of indel-calling. Here -m and -F are used per-sample which enables to detect rare indels in low-coverage bams. Experimental.
Alternative model for multiallelic and rare-variant calling. Proof-of-principle implementation.
Bug fixes
VCF annotations with and without -m and more robust rm_info
Allow filtering by read group or sample name in bamcheck. Bug fix in rm_info.
Fix in output of missing haploid genotypes
Use int64_t to prevent count overflow in view -c; on behalf of Joshua Randall: Set y2range in quals2.png plot
First attempt at updating MPOS in 'samtools depad'
Tweak order free things (avoids an 'samtools depad' seg fault on error)
Fix 'samtools depad' seg-fault when MPOS/PNEXT given but MRNM/RNEXT is not
Merge pull request #14 from peterjc/depad3

Update MPOS/PNEXT during 'samtools depad'
New --GC-depth option to bamcheck. Take into account not so frequent CIGAR codes. Fix in realloc_buffers. Prevent segfault with long command line options; Set xrange correctly in plot-bamcheck coverage.gp
GC-depth calculation now more robust to small GCD bin sizes
Fix in insertion cycle calculation of rev reads
Merge remote branch 'remotes/pd3/master'

Conflicts:
	misc/bamcheck.c
Complain when BAM cannot be open. Severe bug fixed in -m haploid calling.
More user-friendly error output
Changed default reflen; more informative error message when GCD bin size too small or reflen too big
Drop empty bins from coverage distribution
Merge remote branch 'remotes/pd3master/master' into develop