<commit_before>#![feature(vec_resize, path_ext)]
use std::ascii::AsciiExt;
use std::collections::HashMap;
use std::io::Write;
use std::io::stderr;
use std::fs::File;
use std::cmp::{min, max};
use std::str;
use std::path::{PathBuf, Path};
use std::process::Command;
use std::fs::PathExt;

extern crate argparse;
use argparse::{ArgumentParser, StoreTrue, StoreFalse, Store};

extern crate regex;
use regex::Regex;

extern crate rust_htslib;
use rust_htslib::bam::Read;
use rust_htslib::bam::IndexedReader;
use rust_htslib::bam::record::Cigar;

fn cigar2exons(
    exons: &mut Vec<(i32, i32)>,
    cigar: &Vec<Cigar>,
    pos: i32)
{
    let mut pos = pos;
    for op in cigar {
        match op {
            &Cigar::Match(length) => {
                pos += length as i32;
                exons.push((pos - length as i32, pos));
            },
            &Cigar::RefSkip(length) | &Cigar::Del(length) => {
                pos += length as i32;
            },
            &Cigar::Ins(_) | &Cigar::SoftClip(_) | &Cigar::HardClip(_) | &Cigar::Pad(_) => {},
            c => panic!("Bad CIGAR string: {:?}", c)
        };
    }
}

fn open_file(
    options: &Options,
    read_number: i32,
    strand: &str,
    split_strand: &str,
    fhs: &mut HashMap<String,Option<File>>)
    -> String
{
    let mut prefix = PathBuf::new();
    prefix.set_file_name(&options.bamfile);
    prefix.set_extension("");
    let track_name = vec!(
        if !options.trackname.is_empty() {options.trackname.clone()} else {prefix.as_path().to_str().unwrap().to_string()},
        if options.split_read && read_number>0 {format!(".r{}", read_number)} else {"".to_string()},
        if split_strand != "uu" && !strand.is_empty() {format!(".{}", strand)} else {"".to_string()},
        ).connect("");

    let filename = vec!(
        if !options.out.is_empty() {options.out.clone()} else {prefix.as_path().to_str().unwrap().to_string()},
        if options.split_read && read_number>0 {format!(".r{}", read_number)} else {"".to_string()},
        if split_strand != "uu" && !strand.is_empty() {format!(".{}", strand)} else {"".to_string()},
        ".bedgraph".to_string(),
        ).connect("");

    // initialize the file if needed
    if !fhs.contains_key(&filename) {
        let mut f = File::create(&filename).unwrap();
        if options.trackline {
            writeln!(f, "track type=bedGraph name=\"{}\" description=\"{}\" visibility=full", track_name, track_name).unwrap();
        }
        fhs.insert(filename.clone(), Some(f));
    }
    filename
}

fn write_chr(
    options: &Options,
    chr: &(u32, String),
    histogram: &HashMap<(i32,String),Vec<i32>>,
    fhs: &mut HashMap<String,Option<File>>,
    split_strand: &str)
{
   for (key, histo) in histogram {
       let read_number = key.0;
       let strand = &key.1;
       let filename = open_file(options, read_number, strand, split_strand, fhs);

       let ref mut fh = fhs.get_mut(&filename).unwrap().as_mut().unwrap();

       // scan the histogram to produce the bedgraph data
       let mut start: usize = 0;
       let mut end: usize = 0;
       let ref_length: usize = chr.0 as usize;
       while start < ref_length {<commit_msg>connect -> join<commit_after>#![feature(vec_resize, path_ext)]
use std::ascii::AsciiExt;
use std::collections::HashMap;
use std::io::Write;
use std::io::stderr;
use std::fs::File;
use std::cmp::{min, max};
use std::str;
use std::path::{PathBuf, Path};
use std::process::Command;
use std::fs::PathExt;

extern crate argparse;
use argparse::{ArgumentParser, StoreTrue, StoreFalse, Store};

extern crate regex;
use regex::Regex;

extern crate rust_htslib;
use rust_htslib::bam::Read;
use rust_htslib::bam::IndexedReader;
use rust_htslib::bam::record::Cigar;

fn cigar2exons(
    exons: &mut Vec<(i32, i32)>,
    cigar: &Vec<Cigar>,
    pos: i32)
{
    let mut pos = pos;
    for op in cigar {
        match op {
            &Cigar::Match(length) => {
                pos += length as i32;
                exons.push((pos - length as i32, pos));
            },
            &Cigar::RefSkip(length) | &Cigar::Del(length) => {
                pos += length as i32;
            },
            &Cigar::Ins(_) | &Cigar::SoftClip(_) | &Cigar::HardClip(_) | &Cigar::Pad(_) => {},
            c => panic!("Bad CIGAR string: {:?}", c)
        };
    }
}

fn open_file(
    options: &Options,
    read_number: i32,
    strand: &str,
    split_strand: &str,
    fhs: &mut HashMap<String,Option<File>>)
    -> String
{
    let mut prefix = PathBuf::new();
    prefix.set_file_name(&options.bamfile);
    prefix.set_extension("");
    let track_name = vec!(
        if !options.trackname.is_empty() {options.trackname.clone()} else {prefix.as_path().to_str().unwrap().to_string()},
        if options.split_read && read_number>0 {format!(".r{}", read_number)} else {"".to_string()},
        if split_strand != "uu" && !strand.is_empty() {format!(".{}", strand)} else {"".to_string()},
        ).join("");

    let filename = vec!(
        if !options.out.is_empty() {options.out.clone()} else {prefix.as_path().to_str().unwrap().to_string()},
        if options.split_read && read_number>0 {format!(".r{}", read_number)} else {"".to_string()},
        if split_strand != "uu" && !strand.is_empty() {format!(".{}", strand)} else {"".to_string()},
        ".bedgraph".to_string(),
        ).join("");

    // initialize the file if needed
    if !fhs.contains_key(&filename) {
        let mut f = File::create(&filename).unwrap();
        if options.trackline {
            writeln!(f, "track type=bedGraph name=\"{}\" description=\"{}\" visibility=full", track_name, track_name).unwrap();
        }
        fhs.insert(filename.clone(), Some(f));
    }
    filename
}

fn write_chr(
    options: &Options,
    chr: &(u32, String),
    histogram: &HashMap<(i32,String),Vec<i32>>,
    fhs: &mut HashMap<String,Option<File>>,
    split_strand: &str)
{
   for (key, histo) in histogram {
       let read_number = key.0;
       let strand = &key.1;
       let filename = open_file(options, read_number, strand, split_strand, fhs);

       let ref mut fh = fhs.get_mut(&filename).unwrap().as_mut().unwrap();

       // scan the histogram to produce the bedgraph data
       let mut start: usize = 0;
       let mut end: usize = 0;
       let ref_length: usize = chr.0 as usize;
       while start < ref_length {
{'fraction_non_alphanumeric': 0.1782240351427675, 'fraction_numerical': 0.008785691873235017, 'mean_word_length': 3.0144836272040303, 'pattern_counts': {'":': 0, '<': 21, '<?xml version=': 0, '>': 34, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7406700', 'n_tokens_mistral': 2225, 'n_tokens_neox': 2174, 'n_words': 497}