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2024/10/25-11:49:01 (Linux cray unknown)
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@pbenner
pbenner committed Oct 25, 2024
1 parent d4db35a commit c523447
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Showing 5 changed files with 516 additions and 455 deletions.
50 changes: 25 additions & 25 deletions src/bin/bam-to-bigwig.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -28,8 +28,8 @@ use clap::{Arg, ArgAction, Command};
use plotters::prelude::*;

use rustynetics::bigwig::OptionBigWig;
use rustynetics::coverage::OptionCoverage;
use rustynetics::track_generic::GenericTrack;
use rustynetics::track_coverage::OptionBamCoverage;
use rustynetics::track_coverage::bam_coverage;

/* -------------------------------------------------------------------------- */
Expand Down Expand Up @@ -386,7 +386,7 @@ fn main() {

print_stderr!(config, 1, "Verbose mode enabled with level: {}", config.verbose);

let mut options_list: Vec<OptionBamCoverage> = Vec::new();
let mut options_list: Vec<OptionCoverage> = Vec::new();

if let Some(opt_bin_size) = matches.get_one::<String>("bin-size") {
let bin_size : usize = opt_bin_size.parse().unwrap_or_else(|_| {
Expand All @@ -397,7 +397,7 @@ fn main() {
eprintln!("{}", app.render_usage());
process::exit(1);
} else {
options_list.push(OptionBamCoverage::BinSize(bin_size));
options_list.push(OptionCoverage::BinSize(bin_size));
}
}

Expand All @@ -409,7 +409,7 @@ fn main() {
process::exit(1);
}
}
options_list.push(OptionBamCoverage::BinningMethod(opt_binning_method.clone()));
options_list.push(OptionCoverage::BinningMethod(opt_binning_method.clone()));
}

if let Some(opt_pseudocounts) = matches.get_one::<String>("pseudocounts") {
Expand All @@ -420,7 +420,7 @@ fn main() {
}
let t1 = tmp[0].parse::<f64>().expect("Invalid pseudocount value");
let t2 = tmp[1].parse::<f64>().expect("Invalid pseudocount value");
options_list.push(OptionBamCoverage::Pseudocounts([t1, t2]));
options_list.push(OptionCoverage::Pseudocounts([t1, t2]));
}

if let Some(opt_read_length) = matches.get_one::<String>("filter-read-lengths") {
Expand All @@ -435,7 +435,7 @@ fn main() {
eprintln!("{}", app.render_usage());
process::exit(1);
}
options_list.push(OptionBamCoverage::FilterReadLengths([t1, t2]));
options_list.push(OptionCoverage::FilterReadLengths([t1, t2]));
}

if let Some(opt_filter_mapq) = matches.get_one::<String>("filter-mapq") {
Expand All @@ -447,13 +447,13 @@ fn main() {
eprintln!("{}", app.render_usage());
process::exit(1);
}
options_list.push(OptionBamCoverage::FilterMapQ(filter_mapq));
options_list.push(OptionCoverage::FilterMapQ(filter_mapq));
}

if let Some(opt_filter_strand) = matches.get_one::<String>("filter-strand") {
match opt_filter_strand.as_str() {
"+" => options_list.push(OptionBamCoverage::FilterStrand('+')),
"-" => options_list.push(OptionBamCoverage::FilterStrand('-')),
"+" => options_list.push(OptionCoverage::FilterStrand('+')),
"-" => options_list.push(OptionCoverage::FilterStrand('-')),
_ => {
eprintln!("{}", app.render_usage());
process::exit(1);
Expand All @@ -469,24 +469,24 @@ fn main() {
}
let t1 = tmp[0].parse::<usize>().expect("Invalid shift value");
let t2 = tmp[1].parse::<usize>().expect("Invalid shift value");
options_list.push(OptionBamCoverage::ShiftReads([t1, t2]));
options_list.push(OptionCoverage::ShiftReads([t1, t2]));
}

if matches.get_flag("smoothen-control") {
options_list.push(OptionBamCoverage::SmoothenControl(true));
options_list.push(OptionCoverage::SmoothenControl(true));
}

if let Some(opt_smoothen_sizes) = matches.get_one::<String>("smoothen-window-sizes") {
let tmp: Vec<&str> = opt_smoothen_sizes.split(',').collect();
let smoothen_sizes: Vec<usize> = tmp.iter()
.map(|&s| s.parse::<usize>().expect("Invalid smoothen size"))
.collect();
options_list.push(OptionBamCoverage::SmoothenSizes(smoothen_sizes));
options_list.push(OptionCoverage::SmoothenSizes(smoothen_sizes));
}

if let Some(opt_smoothen_min) = matches.get_one::<String>("smoothen-min-counts") {
let t = opt_smoothen_min.parse::<f64>().expect("Invalid minimum counts");
options_list.push(OptionBamCoverage::SmoothenMin(t));
options_list.push(OptionCoverage::SmoothenMin(t));
}

if let Some(opt_bw_zoom_levels) = matches.get_one::<String>("bigwig-zoom-levels") {
Expand All @@ -505,7 +505,7 @@ fn main() {
process::exit(1);
}
}
options_list.push(OptionBamCoverage::NormalizeTrack(opt_normalize_track.to_lowercase()));
options_list.push(OptionCoverage::NormalizeTrack(opt_normalize_track.to_lowercase()));
}

if let Some(opt_fraglen_range) = matches.get_one::<String>("fraglen-range") {
Expand All @@ -516,7 +516,7 @@ fn main() {
}
let t1 = tmp[0].parse::<i32>().expect("parsing fragment length range failed");
let t2 = tmp[1].parse::<i32>().expect("parsing fragment length range failed");
options_list.push(OptionBamCoverage::FraglenRange((t1, t2)));
options_list.push(OptionCoverage::FraglenRange((t1, t2)));
}

if let Some(opt_fraglen_bin_size) = matches.get_one::<String>("fraglen-bin-size") {
Expand All @@ -525,7 +525,7 @@ fn main() {
process::exit(1);
});
if fraglen_bin_size > 0 {
options_list.push(OptionBamCoverage::FraglenBinSize(fraglen_bin_size));
options_list.push(OptionCoverage::FraglenBinSize(fraglen_bin_size));
}
}

Expand All @@ -540,7 +540,7 @@ fn main() {
}

if let Some(opt_filter_chroms) = matches.get_one::<String>("filter-chromosomes") {
options_list.push(OptionBamCoverage::FilterChroms(
options_list.push(OptionCoverage::FilterChroms(
opt_filter_chroms.split(',').map(String::from).collect(),
));
}
Expand All @@ -550,16 +550,16 @@ fn main() {
eprintln!("Invalid initial value specified");
process::exit(1);
});
options_list.push(OptionBamCoverage::InitialValue(value));
options_list.push(OptionCoverage::InitialValue(value));
}

options_list.push(OptionBamCoverage::EstimateFraglen(matches.get_flag("estimate-fragment-length")));
options_list.push(OptionBamCoverage::LogScale(matches.get_flag("log-scale")));
options_list.push(OptionBamCoverage::PairedAsSingleEnd(matches.get_flag("paired-as-single-end")));
options_list.push(OptionBamCoverage::PairedEndStrandSpecific(matches.get_flag("paired-end-strand-specific")));
options_list.push(OptionBamCoverage::FilterDuplicates(matches.get_flag("filter-duplicates")));
options_list.push(OptionBamCoverage::FilterPairedEnd(matches.get_flag("filter-paired-end")));
options_list.push(OptionBamCoverage::FilterSingleEnd(matches.get_flag("filter-single-end")));
options_list.push(OptionCoverage::EstimateFraglen(matches.get_flag("estimate-fragment-length")));
options_list.push(OptionCoverage::LogScale(matches.get_flag("log-scale")));
options_list.push(OptionCoverage::PairedAsSingleEnd(matches.get_flag("paired-as-single-end")));
options_list.push(OptionCoverage::PairedEndStrandSpecific(matches.get_flag("paired-end-strand-specific")));
options_list.push(OptionCoverage::FilterDuplicates(matches.get_flag("filter-duplicates")));
options_list.push(OptionCoverage::FilterPairedEnd(matches.get_flag("filter-paired-end")));
options_list.push(OptionCoverage::FilterSingleEnd(matches.get_flag("filter-single-end")));

config.save_fraglen = matches.get_flag("save-fraglen");
config.save_cross_corr = matches.get_flag("save-crosscorrelation");
Expand Down
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