Add the option for user-defined sample id allowing dots

[jen-dfci]

Changes made to extract.py, genotype.py and merge.py to allow "." in a file name. (e.g. DFCSNKAN.01.bam)

Adds an argument to the extract command called "sample":
arcasHLA extract {sorted.bam file} -t {threads} -v --sample {sampleID} -o {output file}