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
Merged from develop
roh: Allow PLs bigger than 255
Merge branch 'develop' of git://github.com/samtools/bcftools into feature/norm_merge_ids
Merge branch 'develop' of git://github.com/samtools/bcftools into feature/norm_merge_ids
fix for long allele slowdown in normalize_alleles
Fix man page typo
annotate -x INFO drop all header lines. Fixes #98
merge correctly haploid Number=G FORMAT fields
annotate: More informative error message
Merged with develop
Small improvemens and fixes in roh

- do not require -s when there is only one sample in the VCF
- free memory in HMM
- make -M work with -V
- updated man page