riplike: conduct tests

[ArtPoon]

• obtain CRF reference sequences from LANL (https://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html), request Subtype Reference and GENOME
• process CRF genome sequences with riplike and RIP, compare outputs
• documented composition of CRFs can be found here: https://www.hiv.lanl.gov/content/sequence/HIV/CRFs/CRFs.html

[kwade4]

So far, I have tested riplike using:

• Ref.A1.AU.03.PS1044_Day0.DQ676872
• Ref.A2.CD.97.97CDKTB48.AF286238
• Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455
• Ref.C.ET.86.ETH2220.U46016
• Ref.D.CM.01.01CM_4412HAL.AY371157
• Ref.F1.BR.93.93BR020_1.AF005494

So far, riplike seems to be working as expected - best_ref and second_ref are very similar to RIP's output.

[ArtPoon]

Put on hold until we address #17