New command "bcftools convert" with limited functionality
Merged from develop
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.
Write out description and author in each source file header
documentation update

Adjust/relocate the BCF1 and calling text as desired.

* clarify `--phased` option in `bcftools view`. Fixes (#92)
* add some man text about BCF1
* add some man text about calling no with `call` rather than `view`
* add in man doc for recent changes to `bcftools index`
Merge pull request #94 from mcshane/feature/docs

documentation update
Update copyright years to reflect when changes were made

Added the year 2012 to mcall.c's notice, as it contains code from
samtools-0.1.x/bcftools/prob1.c written by Petr Danecek in 2012.

Also write out description and author in each source file header.
Improved filtering via -i/-e

- added new functions (strlen,abs,sum)
- variables (ref,alt,n_alt,n_samples)
- allow functions on both INFO and FORMAT fields
- expressions are now case insensitive (with the exception of tag names)
- dropped the unnecessary prefix "%" as conflicts can be avoided by
giving the full prefix (e.g. INFO/QUAL vs QUAL)
Support for AC, MAC, AF, MAF in filtering expressions
annotate: New --rename-chrs option
Test for annotate --rename-chrs
Updated man page for --rename-chrs
merge: leave QUAL unset if "." in all source files
Add previously-omitted copyright notices

ccall.c contains some code (ttest(), test16(), etc) from
samtools-0.1.x/bcftools/call1.c written by Heng Li while at Broad.

em.c, prob1.c, and prob1.h originate from similarly-named files in
samtools-0.1.x/bcftools (also samtools-0.1.x/bcftools/ld.c for em.c),
originally written by Heng Li at Broad in 2010 and modified thereafter
by him and by others at Sanger.

tabix.c was originally written by Heng Li at Broad in 2012, and modified
thereafter at Sanger.

Also write out description and author in each source file header.