RoH rewritten for greater flexibility, experimental
HMM: A brief usage documentation
RoH: Updated docs, more intuitive variable naming
Merge branch 'develop' into RoH
Merged develop
roh: -M for constant recombination rate; support for

multiple chromosomes with Viterbi training -V
Merged develop
roh bug fix: Use nsites, not args->nsites
New command "bcftools convert" with limited functionality
Merged from develop
Merged from develop
roh: Allow PLs bigger than 255
Updated obsolete error message. Fixes #85
Add copyright notices and licensing boilerplate
Add copyright notices and licensing boilerplate

This file originated as bcftools/vcfutils.pl in the samtools project,
so includes copyright notices reflecting its authorship there.

(See also https://github.com/samtools/samtools)
Add copyright notices and licensing boilerplate

The file bcftools.1 is generated from this file, and it remains to find
a way to have copyright and licensing information generated into it.
Update license file

Rename to LICENSE, as the filename COPYING usually suggests GPL.
(Use git diff -M40% to see this commit as a rename.)

Use the less ambiguous term "MIT/Expat" license, as there are several
different licenses sometimes called the "MIT license".

Add note about year ranges, and reformat the last paragraph -- there
are no text changes.
Set Git attributes similarly to the samtools repository

Mark BAM files (if we add any) as binary and view their diffs as SAM.
Omit control files and README.md from release tarballs.
Run tests using htslib's just-built bgzip and tabix

Use makefile dependencies to ensure bgzip and tabix are up to date,
and (typically) run them via explicit paths to avoid falling back to
already-installed copies.

Add test/test.pl infrastructure to supply explicit bgzip/tabix paths
as required.  Eventually, there will be a Makefile mode to use system
bgzip and tabix along with a system htslib; such a mode will provide
empty $(BGZIP) and $(TABIX) and so "test.pl --exec bgzip= --exec tabix="
invokes executables named "bgzip" and "tabix" via $PATH.
Merge branch 'develop' of git://github.com/samtools/bcftools into feature/norm_merge_ids