<commit_before>---
title: CFE HCV Algorithm
description: version
---

Trimmed.<commit_msg>Debug HCV rules page by replacing some of the content as part of #412.<commit_after>---
title: CFE HCV Algorithm
description: version cfe-hcv 1.5 - 07-Dec-2016
---

Rules are applied for each drug and each genotype found in a sample. Each rule
contains a mutation description, the `=>` symbol, and an action. A mutation
description is the position number of an amino acid within the gene region,
plus a variant amino acid. An exclamation mark in the mutation means any
variant except those listed. A "TRUE" mutation is always applied for that
genotype. An action is either a number that adds to the score, or a name in
quotes. The program adds up all the scores and collects all the names, before
deciding on a resistance report.

* If the score is 4, then it reports "Resistance Possible".
* If the score is 8 or more, then it reports "Resistance Likely".
* If the score is 0 with the "Not available" name, then it reports "Resistance
    Interpretation Not Available".
* If the score is 0 with the "Not indicated" name, then it reports
    "Not Indicated".
* If the score is 0 with the "Effect unknown" name, then it reports "Mutations
    Detected; Effect Unknown".
* If there are gaps in coverage for some of the mutation locations, then it
    reports "Sequence does not meet quality-control standards".
* Otherwise, it reports "Likely Susceptible".

Here are the rules used for each of the drugs.

| Gene | Drug | Genotype | Rules |
|------|------|----------|-------|
| NS3  | Boceprevir (Victrelis™)                                   | 1A | SCORE FROM |
{'fraction_non_alphanumeric': 0.08424242424242424, 'fraction_numerical': 0.01090909090909091, 'mean_word_length': 3.2551546391752577, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 4, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 3, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6135364', 'n_tokens_mistral': 465, 'n_tokens_neox': 428, 'n_words': 246}