Hivmmer

* Add minimum coverage threshold when calling consensus sequence. (issue-11)

* Filters HMMER alignments using optimal E-value thresholds determined
through a validation study. (issue-7)
* Includes prepackaged pHMMs for whole HIV genome. (issue-8)
* Re-implemented the main hivmmer script in python and added support for
whole-genome alignment and additional reporting output. (issue-9)
* Improves the consistency of whole-genome coverage by passing all translated
sequences to HMMER, and removing alignments with stop codons after alignment.
This approach retains reads that span one or more genes in different frames,
which were dropped in the previous approach since they would have stop codons
in the region of the read lying in the other frame. (issue-10)

* Added an output file listing the frequency of specific insertion codons at
each site (issue-1).
* Replaced the fastx_collapser stage with a new QC filtering stage that
implements a read length filter (>75) and mean PHRED score filter (>25), and
performs deduplication like fastx_collapser (issue-6).