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.
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.
Add a few comments to bam merging function
WIP on header merging
Add target id translation code and write pseudo code for building RG and PG translation tables
Convert PG and RG pseudo code to working code.
Add pseudocode for PG PP: translation.
Add -D_GNU_SOURCE for some of the newer POSIX functions
Add copyright header
Add code to append SQ tags to header
Fix asprintf format specifiers
Fix bugs picked up by unit testing.
Make trans_tbl_t a named struct and move aside variable names the same as it.
More work on merging @RG and @PG tags into header.
Unit tests for merge
add skeleton code for PP processing
NULLify some freed pointers.
Add tracing statement
Unit test trans_tbl_init add test 5 for PG tags
Fix memory leaks and finalise @PG PP handling