Allow merging snps(indels) and combined variants with -m both
More info in verbose polysomy output; reversed meaning of -p
query: Support dots in tag names. Resolves #174
query: Support dots in tag names. Resolves #174
reheader works on streamed input again
view: Major/nonmajor allele count filters
manpage: Replaced problematic "^" with "&#94;"
polysomy: Output estimated fraction of affected cell with -v
Simple tests for view -c/C major/nonmajor
Simple tests for view -c/C major/nonmajor
Bugfix in merging MNP records, updated man page. Resolves #166
stats: Accept the default -c none value on command line as well. Resolves #145
Merge pull request #176 from travc/develop

Basic tests for view -c/C major
plot-vcfstats: separate data from plot.py + fixes #179
Use the right type in realloc()
Add support for <DEL> in bcf-consensus

The code now reads <DEL> in the ALT allele as a valid exception.

*NOTE* Bug in mask_region functionality. Apparently this happens when
a variant (a deletion) removes sequence from the next FASTA line.
This results in masking happening one line too far. Second
test_consensus fails now.
New -c/--chain option in bcftools-consensus

This option saves the transformation of the reference to the
consensus sequence in a chain file that can be used with the
liftOver tool.
Bug fixes in consensus

- the position of a symbolic allele marks the coordinate *before* the event
- mask_region coordinates did not take into account indels
- updated tests which seemed wrong.

Note: This needs further review, more bugs likely!
Merge remote-tracking branch 'upstream-develop'