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.
Reinstate bam_iter_read(iter=NULL) reading the whole file

The old samtools API defined iter=NULL to mean to iterate over all
records with bam_read1(), which was assumed by bam_merge_core2() and
possibly third-party code.  Htslib iterators (currently) just segfault
with iter=NULL, so the previous simple shim accidentally broke this.

Fixes #83, though this will be refixed when the native htslib-API-based
samtools merge branch lands.
Fix annoying memset warning and bug in md5.c
Fix error in bam.h comment
mpileup: Fix SGB numerical underflow; Output correct samtools version on output
mpileup: Added forgotten #include
mpileup: Prevent under/overflow of the SGB annotation
mpileup: Updated tests to reflect SGB change
Fix CRLF-style line termination

Fixes #76.
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()