pandora_lib_promethion/:

// reference="/data/ref/hs1/chm13v2.0.fa"
// bcftools="/data/tools/bcftools-1.18/bcftools"
//
// DIAG_CASE_DIR="/data/longreads_basic_pipe/${name}/diag"
// MRD_CASE_DIR="/data/longreads_basic_pipe/${name}/mrd"
//
// DIAG_OUTPUT_DIR="${DIAG_CASE_DIR}/nanomonsv"
// MRD_OUTPUT_DIR="${MRD_CASE_DIR}/nanomonsv"
//
// DIAG_BAM="${DIAG_CASE_DIR}/${name}_diag_hs1.bam"
// MRD_BAM="${MRD_CASE_DIR}/${name}_mrd_hs1.bam"
//
// DIAG_OUT_PREFIX="${DIAG_OUTPUT_DIR}/${name}_diag"
// MRD_OUT_PREFIX="${MRD_OUTPUT_DIR}/${name}_mrd"
//
// if [ ! -d "$DIAG_OUTPUT_DIR" ]; then
//   mkdir "$DIAG_OUTPUT_DIR"
// fi
//
// if [ ! -d "$MRD_OUTPUT_DIR" ]; then
//   mkdir "$MRD_OUTPUT_DIR"
// fi
//
// # PARSE
// if [ ! -f "${DIAG_OUT_PREFIX}.bp_info.sorted.bed.gz" ]; then
//   nanomonsv parse --reference_fasta "$reference" "$DIAG_BAM" "$DIAG_OUT_PREFIX"
// fi
//
// if [ ! -f "${MRD_OUT_PREFIX}.bp_info.sorted.bed.gz" ]; then
//   echo "[pipe] NanomonSV parse ${MRD_BAM}"
//   nanomonsv parse --reference_fasta "$reference" "$MRD_BAM" "$MRD_OUT_PREFIX"
// fi
//
// # GET
// if [ ! -f "${DIAG_OUT_PREFIX}.nanomonsv.result.vcf" ]; then
//   nanomonsv get --control_prefix "$MRD_OUT_PREFIX" \
//     --control_bam "$MRD_BAM" \
//     --processes 155 \
//     "$DIAG_OUT_PREFIX" \
//     "$DIAG_BAM" "$reference"
// fi
//
// # GET MRD
// if [ ! -f "${MRD_OUT_PREFIX}.nanomonsv.result.vcf" ]; then
//   nanomonsv get \
//     --processes 155 \
//     "$MRD_OUT_PREFIX" \
//     "$MRD_BAM" "$reference"
// fi
//
// vcf_passed="${DIAG_OUT_PREFIX}_nanomonsv_PASSED.vcf.gz"
// if [ ! -f "$vcf_passed" ]; then
//   $bcftools sort "${DIAG_OUT_PREFIX}.nanomonsv.result.vcf" | \
//     $bcftools view -s "TUMOR" --write-index --threads 20 \
//     -i "FILTER='PASS'" \
//     -o "$vcf_passed"
// fi

use std::{
    fs,
    io::{BufRead, BufReader},
    path::Path,
    process::{Command, Stdio},
    sync::{Arc, Mutex},
    thread,
};

use log::info;

use crate::commands::bcftools::{bcftools_keep_pass, BcftoolsConfig};

#[derive(Debug)]
pub struct NanomonSVConfig {
    pub bin: String,
    pub result_dir: String,
    pub reference: String,
    pub thread: u8,
}

impl Default for NanomonSVConfig {
    fn default() -> Self {
        Self {
            bin: "nanomonsv".to_string(),
            result_dir: "/data/longreads_basic_pipe".to_string(),
            reference: "/data/ref/hs1/chm13v2.0.fa".to_string(),
            thread: 155,
        }
    }
}

#[derive(Debug)]
pub struct NanomonSV {
    pub id: String,
    pub diag_bam: String,
    pub mrd_bam: String,
    pub diag_out_dir: String,
    pub mrd_out_dir: String,
    pub log: String,
    pub config: NanomonSVConfig,
}

impl NanomonSV {
    pub fn new(id: &str, diag_bam: &str, mrd_bam: &str, config: NanomonSVConfig) -> Self {
        let diag_out_dir = format!("{}/{id}/diag/nanomonsv", &config.result_dir);
        let mrd_out_dir = format!("{}/{id}/mrd/nanomonsv", &config.result_dir);

        NanomonSV {
            id: id.to_string(),
            diag_bam: diag_bam.to_string(),
            mrd_bam: mrd_bam.to_string(),
            diag_out_dir,
            mrd_out_dir,
            log: String::default(),
            config,
        }
    }

    pub fn run(&mut self) {
        // Create direcories
        if !Path::new(&self.diag_out_dir).exists() {
            fs::create_dir_all(&self.diag_out_dir).unwrap();
        }
        if !Path::new(&self.mrd_out_dir).exists() {
            fs::create_dir_all(&self.mrd_out_dir).unwrap();
        }

        // Parse
        let diag_out_prefix = format!("{}/{}_diag", self.diag_out_dir, self.id);
        let mrd_out_prefix = format!("{}/{}_mrd", self.mrd_out_dir, self.id);

        let diag_info_vcf = format!("{diag_out_prefix}.bp_info.sorted.bed.gz");
        let mrd_info_vcf = format!("{mrd_out_prefix}.bp_info.sorted.bed.gz");

        let log: Arc<Mutex<String>> = Arc::new(Mutex::new(String::default()));

        let mut threads_handles = Vec::new();
        if !Path::new(&diag_info_vcf).exists() {
            let bin = self.config.bin.clone();
            let reference = self.config.reference.clone();
            let diag_bam = self.diag_bam.clone();
            let log = log.clone();
            let diag_out_prefix = diag_out_prefix.clone();

            let handle = thread::spawn(move || {
                let mut child = Command::new(bin)
                    .args([
                        "parse",
                        "--reference_fasta",
                        &reference,
                        &diag_bam,
                        &diag_out_prefix,
                    ])
                    .stdout(Stdio::piped())
                    .stderr(Stdio::inherit())
                    .spawn()
                    .expect("Failed to spawn NanomonSV parse");

                if let Some(stdout) = child.stdout.take() {
                    let reader = BufReader::new(stdout);
                    for line in reader.lines().map_while(Result::ok) {
                        info!("{}", line);
                        let mut log_lock = log.lock().unwrap();
                        log_lock.push_str(&line);
                        log_lock.push('\n');
                    }
                }
            });
            threads_handles.push(handle);
        }

        if !Path::new(&mrd_info_vcf).exists() {
            let bin = self.config.bin.clone();
            let reference = self.config.reference.clone();
            let mrd_bam = self.diag_bam.clone();
            let log = log.clone();
            let mrd_out_prefix = mrd_out_prefix.clone();

            let handle = thread::spawn(move || {
                let mut child = Command::new(bin)
                    .args([
                        "parse",
                        "--reference_fasta",
                        &reference,
                        &mrd_bam,
                        &mrd_out_prefix,
                    ])
                    .stdout(Stdio::inherit())
                    .stderr(Stdio::piped())
                    .spawn()
                    .expect("Failed to spawn NanomonSV parse");

                if let Some(stdout) = child.stderr.take() {
                    let reader = BufReader::new(stdout);
                    for line in reader.lines().map_while(Result::ok) {
                        info!("{}", line);
                        let mut log_lock = log.lock().unwrap();
                        log_lock.push_str(&line);
                        log_lock.push('\n');
                    }
                }
                child.wait().unwrap();
            });
            threads_handles.push(handle);
        }

        // Wait for all threads to finish
        for handle in threads_handles {
            handle.join().expect("Thread panicked");
        }

        // Get
        let diag_result_vcf = format!("{diag_out_prefix}.nanomonsv.result.vcf");
        let mrd_result_vcf = format!("{mrd_out_prefix}.nanomonsv.result.vcf");

        if !Path::new(&mrd_result_vcf).exists() {
            let mut child = Command::new(&self.config.bin)
                .args([
                    "get",
                    "--process",
                    &self.config.thread.to_string(),
                    &mrd_out_prefix,
                    &self.mrd_bam,
                    &self.config.reference,
                ])
                .stdout(Stdio::inherit())
                .stderr(Stdio::piped())
                .spawn()
                .expect("Failed to spawn nanomonsv");

            if let Some(stdout) = child.stderr.take() {
                let reader = BufReader::new(stdout);
                for line in reader.lines().map_while(Result::ok) {
                    info!("{line}");
                    let mut log_lock = log.lock().unwrap();
                    log_lock.push_str(&line);
                    log_lock.push('\n');
                }
            }

            child.wait().unwrap();
        }

        if !Path::new(&diag_result_vcf).exists() {
            let mut child = Command::new(&self.config.bin)
                .args([
                    "get",
                    "--control_prefix",
                    &mrd_out_prefix,
                    "--control_bam",
                    &self.mrd_bam,
                    "--process",
                    &self.config.thread.to_string(),
                    &diag_out_prefix,
                    &self.diag_bam,
                    &self.config.reference,
                ])
                .stdout(Stdio::inherit())
                .stderr(Stdio::piped())
                .spawn()
                .expect("Failed to spawn nanomonsv");

            if let Some(stdout) = child.stderr.take() {
                let reader = BufReader::new(stdout);
                for line in reader.lines().map_while(Result::ok) {
                    info!("{line}");
                    let mut log_lock = log.lock().unwrap();
                    log_lock.push_str(&line);
                    log_lock.push('\n');
                }
            }

            child.wait().unwrap();
        }

        let vcf_passed = format!("{diag_out_prefix}_nanomonsv_PASSED.vcf.gz");
        if !Path::new(&vcf_passed).exists() {
            bcftools_keep_pass(&diag_result_vcf, &vcf_passed, BcftoolsConfig::default()).unwrap();
        }
    }
}