Fix whitespace inconsistancy and add license to bam_tview.c.
Create README.md
Merge branch 'develop' of git://github.com/samtools/samtools into develop
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.
Add an unoptimised GCC C99 build

This build complains about plain (non-static) inline functions, whose
interpretation differs between gcc -std=gnu90 and C99.  (Ideally we'd
use -std=c99, but that also suppresses declarations for standard but
non-C-standard functions like strdup() and getopt() and always fails.)

Also redo the htslib subproject as a before_script, so $HTSDIR trivia
doesn't appear in the build matrix and we're not overriding the install
script (though that's not being otherwise used anyway).
Use static inline, not just inline

Define these as static inline in the C99-approved way.  Fixes #82.
Merge branch 'develop' of git://github.com/samtools/samtools into develop