pub fn run_variant_calling_pipeline(
    ref_name: &str,
    reads_names: Reads,
    result_dir: &str,
    bwa_threads: u16,
) {
    utils::bwa_index_if_required(ref_name);
    utils::bwa_mem_align(
        ref_name,
        &reads_names.clone(),
        &format!("{}/raw_alignments.sam", result_dir)[..],
        bwa_threads,
    );
    samtools_fixmate(result_dir);
    samtools_sort(result_dir);
    freebayes_variant_call(ref_name, result_dir);
}
// run the entire pipeline, one step after another
// everything must be blocking since each step depends on the previous step's output
run the entire pipeline, one step after another
everything must be blocking since each step depends on the previous step's output
run the entire pipeline one step after another everything must be blocking since each step depends on the previous step ' s output
pub fn run_variant_calling_pipeline(
    ref_name: &str,
    reads_names: Reads,
    result_dir: &str,
    bwa_threads: u16,
) {
    utils::bwa_index_if_required(ref_name);
    utils::bwa_mem_align(
        ref_name,
        &reads_names.clone(),
        &format!("{}/raw_alignments.sam", result_dir)[..],
        bwa_threads,
    );
    samtools_fixmate(result_dir);
    samtools_sort(result_dir);
    freebayes_variant_call(ref_name, result_dir);
}
pub fn run_variant_calling_pipeline ( ref_name : & str , reads_names : Reads , result_dir : & str , bwa_threads : u16 , ) { utils :: bwa_index_if_required ( ref_name ) ; utils :: bwa_mem_align ( ref_name , & reads_names . clone ( ) , & format ! ( " " result_dir ) [ .. ] , bwa_threads , ) ; samtools_fixmate ( result_dir ) ; samtools_sort ( result_dir ) ; freebayes_variant_call ( ref_name , result_dir ) ; }
run the entire pipeline, one step after another
everything must be blocking since each step depends on the previous step's output
run the entire pipeline one step after another everything must be blocking since each step depends on the previous step ' s output
ref_name
&str
reads_names
Reads
result_dir
&str
bwa_threads
u16
ref_name
&str
reads_names
Reads
result_dir
&str
bwa_threads
u16