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
vcfnorm: when merging records, average QUALs and accumulate IDs and FILTERs

- when merging records with `norm -m+`, IDs were getting removed. This
  fixes that.
- FILTER was being taken from the first record seen. This would make it
  so that if any records FAIL, the site FAILs. Could add option to say
  that if any record PASSes, then PASS the entire site
- average the QUALs over records
New command "bcftools convert" with limited functionality
Merged from develop
Merged from develop
roh: Allow PLs bigger than 255
Merge branch 'develop' of git://github.com/samtools/bcftools into feature/norm_merge_ids
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)
Merge branch 'develop' of git://github.com/samtools/bcftools into feature/norm_merge_ids
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