Function run 

pub fn run(
    in_bam: String,
    out_bam: String,
    inverse: bool,
    both_end: f64,
    left_side: f64,
    right_side: f64,
    unalign: bool,
) -> Result<u8, String>

Workflow to process an input bam file and write the pass-filter alignments into a new bam file

Arguments

• in_bam: input bam file
• out_bam: output bam file
• inverse: boolean flag to indicate whether we want to write out the failed-filter alignments only
• both_end: maximum fraction of total clipped bases relative to the read sequence length to consider as pass
• left_side: maximum fraction of of clipped bases on either side relative to the read sequence length to consider as pass
• right_side: maximum fraction of of clipped bases on either side relative to the read sequence length to consider as pass

Examples

use filter_clipped::run;
use rust_htslib::bam;
use rust_htslib::bam::Read;
fn count_bam(bam_file: String, expected_count: i32) {
    // helper function to verify result
    let mut bam_reader = bam::Reader::from_path(bam_file).unwrap();
    let mut aln_count = 0;
    for r in bam_reader.records() {
        let _record = r.unwrap();
        aln_count += 1;
    }
    assert_eq!(expected_count, aln_count);
}

let out_bam = "out.sam";
run(
    "test/data/test.sam".to_string(),
    out_bam.to_string(),
    false,
    0.1,
    0.1,
    0.1,
    false,
    );
count_bam(out_bam.to_string(), 6);