Some performance
mmm...plumbing
Tests
Simplify
Include htslib in our build directory

Eventually perhaps we'll be able to install an htslib-dev package
during before_install instead.
Include htslib rules and add header dependencies

Use the rules and variables from htslib.mk to write out exact
dependencies on htslib headers and (for executables) library.
With this, samtools builds with "make" from here are correct
even when htslib source code is being modified.

(A little more infrastructure is needed to select between static
and shared libhts.)
Use indexed implementation from useful
README
Merge remote-tracking branch 'origin/consensus-align'
Added BGZF indexing and reindexing capability to bgzip. Fixed -b seeking.
Added a test suite for samtools, currently faidx and bgzip are tested.
Added a test suite for samtools, currently faidx and bgzip are tested.
tview and bgzip: Check that the files are bgzipped, not gzipped.
constify input parameter to faidx_fetch_seq
Fix buglet: initialise the kstring_t

Also parse "" rather than NULL in the unlikely event of an empty .fai
file, and add a bam_import.o prerequisite that was omitted.
Faster interval queries
Merge pull request #62 from jts/develop

constify input parameter to faidx_fetch_seq
Fanicer subcommands
More idiomatic record constructors
Warn and use correct bin when bin field is wrong

The abort introduced in pull request #43 (8e3b3f2 "Verify old BIN value
of reads during 'samtools index'") is too Draconian, as this field is
in practice used only during indexing -- so the BAM file is mostly fine.

If we're recalculating it here anyway, we might as well use the corrected
value to generate the index and just warn (in a rate-limited way) about
the anomalous records.