Create the 'mGEMS' executable

[tmaklin]

All commands should be merged under a single 'mGEMS' executable. Proposed behaviour:

• ./mGEMS — run everything.
• ./mGEMS read — process the alignment files.
• ./mGEMS assign — assign the reads to the references.
• ./mGEMS filter — create the samples.

[ahonkela]

Sounds like a good plan, but maybe the verbs could be rethought. The verbs and descriptions are quite different and some of the proposed verbs might have other conflicting meanings.

[tmaklin]

It's more that the descriptions in my original issue were written as reminders for me and are kind of bad:

• The 'read' program (currently read_files) reads the alignment files in and writes some extra information that isn't directly available in the alignments.
• The 'assign' program (currently assign_reads) assigns the reads in the original sample to the reference lineages and writes the assignments for groups that are requested.
• The 'filter' (currently build_sample) program filters the set of the original reads based on the output from the 'assign' program and writes the assigned reads to corresponding files.

Feel free to suggest better names; however I imagine most users want the filtered reads and thus there shouldn't really be a need for them to run any of the subprograms. They are there mostly for us to use in development.

[tmaklin]

Solved in #5 . The commands are mGEMS bin (bin reads) and mGEMS extract (extract bins from mixed sample).