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

Remove indentation for consistency, and so diffs and viewing with
visible control characters fit better in an 80 column terminal.
mcall: Prevent -0 in QUAL output; clean old unused lk2 stuff
annotate: Fix off-by-one error + tests and docs
Merge copyright notice and licensing boilerplate corrections
Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT

Expand tabs as spaces; hard tab characters are no longer to be used
as there is disagreement as to how many columns they should expand to.
Remove trailing whitespace at the end of lines.

After this commit, please do not commit hard tab characters or trailing
whitespace in .c, .h, .pl, or .txt files, and please consider using a
pre-commit hook in your local repository to enforce this.

These steps will minimise the incidental whitespace changes unrelated
to the intended commit changes that make viewing diffs and merging
less convenient.

To compare files prior to and after the whitespace discontinuity of
this commit, use "diff -b" or "diff -w", "blame -w", etc.

(This does not apply to kmin.[ch], which are in theory synchronised with
kmath.[ch] in the klib project, so minimising differences with copies of
this code elsewhere is more important.  Please avoid accidental incidental
whitespace changes in these files too.)