HACKING.md: add profiling tips
common: add GetDurationString function to pretty-format duration.
mains: use GetDurationString function to show elapsed time.
Common: new function to pretty-print running time infomration
RunInfo: add variable to count units (Reads/pairs) processed.
lobSTR: pretty-print running time information.
lobSTR: print either "reads" or "pairs" in progress report.
Make include flank the default. change using flag --dont-include-flank
adding missing return statement in allelotyper. if no aligned reads don't process that locus
Merge pull request #16 from agordon/minor_improvements

Minor improvements
just print warning for using rmdup with multiple samples ans set it to false
Merge branch 'master' of https://github.com/mgymrek/lobstr-code
fixing problem of negative alleles for --annotation