Fix compilation with the Clang compiler.
Fix type mismatches between types in sizeof() in malloc/calloc/realloc calls. This generates a warning in the clang analyzer, designed to catch incorrectly sized memory allocations.

The allocation at bam_plcmd.c:208 is twice as big as it needs to be, and has been fixed.
Free the outer struct last
Merge branch master of git://github.com/leecbaker/samtools

Some of the files in the original PR have moved to the bcftools repository,
and the remaining type mismatches of this kind have been fixed there.
Use floor(x+0.5) instead of C99's round()
Fixed GCC section so that read cycle column begins with 1 instead of 0.
Merge pull request #95 from wtsi-hgi/develop

Fixed GCC section of stats so that read cycle column begins with 1 instead of 0.
mpileup: Allow up to five alleles (N,A,C,G,T)
Rearrange (so tags can see main_depth()) [minor]
Remove incorrect parameter check

The q parameter is an m*m matrix, and is allocated by the caller and
m & q are passed in accordingly.  It appears that this check may have been
intended to be "if (m > qmax)" but we have no independent idea of the size
of q, so there's no way to validate m against it.

Values in q are computed from aux.bsum[k]/etc where 0 <= k < m, so m is
also limited by the size of bsum[], namely 16.  However meaningful indices
for bsum/etc mostly are 0...4 (i.e., A,C,G,T,N) and in practice (currently)
m is either 4 or 5 (with q sized accordingly).  So checking "if (m > 16)"
would be somewhat pointless.
New "flags" command plus moved filtering from htslib/pileup to BAM reading callbacks
On behalf of Peter Chines, test that filter mask replaces (not just adds to) default mask
mpileup: Disabled CDF version of MWU annotations and made it optional at compile time
Merge branch 'develop' into calling