Add fragment file region scoring matrix creation #38
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donaldcampbelljr
approved these changes
Oct 22, 2024
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| .arg(arg!(--mode <mode>)) | ||
| .arg(arg!(--output <output>)) | ||
| .arg(arg!(--whitelist <whitelist>)) |
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Should we add more info here? Like is it required/help/etc?
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| let mode = match matches.get_one::<String>("mode") { | ||
| Some(mode) => ScoringMode::from_str(mode), | ||
| None => Ok(DEFAULT_SCORING_MODE), | ||
| }; | ||
| let mode = mode.unwrap_or(DEFAULT_SCORING_MODE); |
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These lines seem redundant. Do you actually need line 48?
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| #[rstest] | ||
| fn test_igd_create() { | ||
| let tempdir = tempfile::tempdir().unwrap(); | ||
| let path = PathBuf::from(&tempdir.path()); | ||
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| let db_path_unwrapped = path.into_os_string().into_string().unwrap(); | ||
| let db_output_path = db_path_unwrapped; | ||
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| let path_to_crate = env!("CARGO_MANIFEST_DIR"); | ||
| let testfilelists = format!("{}{}", path_to_crate, "/tests/data/igd_file_list/"); | ||
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| let demo_name = String::from("demo"); | ||
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| create_igd_f(&db_output_path, &testfilelists, &demo_name); | ||
| } | ||
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| #[rstest] | ||
| fn test_igd_parse_bed_file() { | ||
| // Given some random line from a bed file... | ||
| let bed_file_string = | ||
| String::from("chr1 32481 32787 SRX4150706.05_peak_1 92 . 7.69231 13.22648 9.25988 155"); | ||
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| //Placeholder start and end values | ||
| let mut start = 0; | ||
| let mut end = 0; | ||
| let mut va = 0; | ||
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| let result = parse_bed(&bed_file_string, &mut start, &mut end, &mut va).unwrap(); // this will return | ||
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| let unwrapped_result = result.as_str(); | ||
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| assert_eq!(unwrapped_result, "chr1"); | ||
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| // Ensure start and end is modified via parse_bed | ||
| assert_eq!(start, 32481); |
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Why are these igd tests showing up here as new?
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