New test and updated VCF header samtools command string
MWU correction for ties
stats: Removed unused stats code (NMQ)
mpileup: Updated to the latest htslib API; disabled tie correction in MWU for now, as the results look suspicious
mpileup: Updated to htslib vcf module changes
Resolved merge conflicts
Merge branch 'develop' of github.com:samtools/samtools into develop
Also run our tests
Set Git attributes for BAM files in the repository
Add help command and --version options

Rearrange version.h inclusion -- only bamtk.c should #include version.h
so that only one translation unit needs recompiling due to changes in it.

Separate samtools_version() and hts_version() so that they can be displayed
in a more user-friendly way where appropriate.  (--version-only uses
punctuation other than %s:%s as it's likely to be embedded in executable
paths and ":" is a shell semi-metacharacter.)
Write samtools --help output to stdout
Ensure $HTSDIR is used by "make test" too
Remove bcftools, SAM, and VCF sections from man page

The bcftools sections are moving to bcftools.1 in the bcftools project
to be alongside the code they document, while the file format summaries
are moving to htslib, alongside the code that reads/writes them.
Fix whitespace inconsistancy and add license to bam_tview.c.
Create README.md
Detect input format and add samtools view -C option

Just use hts_open("r") to auto-detect the input file format.
Add -C option to specifiy CRAM output.
Add "make install" target
Add omitted non-Perl misc/ programs

We'll carry on ignoring r2plot.lua and vcfutils.lua for now.
Correct reverse complements of CG and AT

6=S=CG and 9=W=AT are each their own complement.
This table can be generated and verified via a small script:

print join(", ", map {($_&1)<<3 | ($_&2)<<1 | ($_&4)>>1 | ($_&8)>>3} 0..15);

Fixes samtools/htslib#5
Fix old API samopen() wrapper fn_aux bugs

For reading, the old samopen()'s third parameter is a FAI filename for
use if sequence headers are missing from the input file; for writing,
it is the headers that are to be written out.

It's not too clear what hts_open()'s third argument is for, but it's
certainly not for output headers.  So pass it as NULL when writing.

Also call sam_hdr_write() for the is_cram case too.