Move HCV resistance report into MiCall pipeline

[donkirkby]

Convert the HCV scoring algorithm to use the Stanford ASI rules format with extensions.

The current algorithm is implemented here:

• fdrive/RESIST/ruby/ckwlib/hcv_algorithm.rb

The driver script is fdrive/RESIST/MISEQ/miseq_gen_results.rb.

• convert rules
• change report title and small print from HIV to HCV
• add drug names
• display genotype
• display multiple genotypes, one per page
• decide how to display drugs with no rules for the given genotype (Not Indicated: genotype X)
• add failure report (rules in comment below)
• add unknown mutation rules
• special rules for 6e: "resistance likely" and "resistance interpretation not available"
• combine midi overlap
• display "not indicated" even when region has bad coverage
• compare results to Ruby version
• update BaseSpace driver to use new HCV rules
• display HCV rules in web page on MiCall web site
• move key coverage positions into scoring algorithm (moved to Get key positions from resistance rules #431)

[donkirkby]

Summary of email discussion with Anita and others about failure scenarios:

1. One genotype has good coverage on NS3, NS5a, NS5b, and other genotypes have bad coverage. Display the genotype with the good coverage, and ignore the genotypes with bad coverage.
2. No genotypes have good coverage, and some genotypes have bad coverage. Display a one-page failure report with a message, "sequence does not meet quality-control standards".
3. Nothing mapped. Same as sampleSheetParser fails to parse combined sample names #2
4. One genotype has good coverage on some regions and bad coverage on others. For example, good coverage on NS3 and NS5a, bad coverage on NS5b. Display the resistance calls for drugs in the good regions, and display "sequence does not meet quality-control standards" for drugs in the bad regions.

There is a special rule for genotype 6e with Sofosbuvir (Epclusa): it should display the message, "resistance interpretation not available".