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
Merged from develop
roh: Allow PLs bigger than 255
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
roh: reset counts with next chromosome
annotate: Do not remove ID if absent in src but present in dst
New format to bcftools convert: --tsv2vcf
Added to the list of authors, sorted alphabetically
Resolved merged conflicts
Updated man page: how to annotate Flag type
New cnv command for copy number variation
cnv: Allow file streams