oarfish 0.6.2

use clap::Parser;
use std::num::NonZeroUsize;

use anyhow::Context;

use core::ffi;
use minimap2_sys as mm_ffi;
use minimap2_temp as minimap2;
use num_format::{Locale, ToFormattedString};
use std::{fs::File, io};

use tracing::info;
use tracing_subscriber::{filter::LevelFilter, fmt, prelude::*, EnvFilter};

use noodles_bam as bam;
use noodles_bgzf as bgzf;
use noodles_sam::header::record::value as header_val;
use noodles_sam::header::record::value::Map as HeaderMap;

mod alignment_parser;
mod bootstrap;
mod bulk;
mod em;
mod prog_opts;
mod single_cell;
mod util;

use crate::prog_opts::{Args, FilterGroup, SequencingTech};
use crate::util::normalize_probability::normalize_read_probs;
use crate::util::oarfish_types::{AlignmentFilters, TranscriptInfo};
use crate::util::{binomial_probability::binomial_continuous_prob, kde_utils};

type HeaderReaderAligner = (
    noodles_sam::header::Header,
    Option<bam::io::Reader<bgzf::MultithreadedReader<File>>>,
    Option<minimap2::Aligner>,
);

fn get_aligner_from_args(args: &Args) -> anyhow::Result<HeaderReaderAligner> {
    info!("read-based mode");

    // set the number of indexing threads
    let idx_threads = &args.threads.max(1);

    // if the user requested to write the output index to disk, prepare for that
    let idx_out_as_str = args.index_out.clone().map_or(String::new(), |x| {
        x.to_str()
            .expect("could not convert PathBuf to &str")
            .to_owned()
    });
    let idx_output = args.index_out.as_ref().map(|_| idx_out_as_str.as_str());

    // create the aligner
    let mut aligner = match args.seq_tech {
        Some(SequencingTech::OntCDNA) | Some(SequencingTech::OntDRNA) => {
            minimap2::Aligner::builder()
                .with_index_threads(*idx_threads)
                .with_cigar()
                .map_ont()
                .with_index(
                    &args
                        .reference
                        .clone()
                        .expect("must provide reference sequence"),
                    idx_output,
                )
                .expect("could not construct minimap2 index")
        }
        Some(SequencingTech::PacBio) => minimap2::Aligner::builder()
            .with_index_threads(*idx_threads)
            .with_cigar()
            .map_pb()
            .with_index(
                &args
                    .reference
                    .clone()
                    .expect("must provide reference sequence"),
                idx_output,
            )
            .expect("could not construct minimap2 index"),
        Some(SequencingTech::PacBioHifi) => minimap2::Aligner::builder()
            .with_index_threads(*idx_threads)
            .with_cigar()
            .map_hifi()
            .with_index(
                &args
                    .reference
                    .clone()
                    .expect("must provide reference sequence"),
                idx_output,
            )
            .expect("could not construct minimap2 index"),
        None => {
            anyhow::bail!("sequencing tech must be provided in read mode, but it was not!");
        }
    };

    info!("created aligner index opts : {:?}", aligner.idxopt);
    // get the best 100 hits
    aligner.mapopt.best_n = args.best_n as i32;
    aligner.mapopt.seed = 11;

    let mmi: mm_ffi::mm_idx_t = unsafe { **aligner.idx.as_ref().unwrap() };
    let n_seq = mmi.n_seq;

    info!(
        "index contains {} sequences",
        n_seq.to_formatted_string(&Locale::en)
    );

    let mut header = noodles_sam::header::Header::builder();

    #[derive(Debug, PartialEq, Eq)]
    pub struct SeqMetaData {
        pub name: String,
        pub length: u32,
        pub is_alt: bool,
    }

    // TODO: better creation of the header
    for i in 0..mmi.n_seq {
        let _seq = unsafe { *(mmi.seq).offset(i as isize) };
        let c_str = unsafe { ffi::CStr::from_ptr(_seq.name) };
        let rust_str = c_str.to_str().unwrap().to_string();
        header = header.add_reference_sequence(
            rust_str,
            HeaderMap::<header_val::map::ReferenceSequence>::new(NonZeroUsize::try_from(
                _seq.len as usize,
            )?),
        );
    }

    header = header.add_program(
        "minimap2-rs",
        HeaderMap::<header_val::map::Program>::default(),
    );

    let header = header.build();
    Ok((header, None, Some(aligner)))
}

fn get_filter_opts(args: &Args) -> anyhow::Result<AlignmentFilters> {
    // set all of the filter options that the user
    // wants to apply.
    match args.filter_group {
        Some(FilterGroup::NoFilters) => {
            info!("disabling alignment filters.");
            // override individual parameters if the user passed them in explicitly
            let fpc = args
                .five_prime_clip
                .provided_or_u32("overriding 5' clip with user-provided value", u32::MAX);
            let tpc = args
                .three_prime_clip
                .provided_or_i64("overriding 3' clip with user-provided value", i64::MAX);
            let st = args
                .score_threshold
                .provided_or_f32("overriding score threshold with user-provided value", 0_f32);
            let maf = args.min_aligned_fraction.provided_or_f32(
                "overriding min aligned fraction with user-provided value",
                0_f32,
            );
            let mal = args.min_aligned_len.provided_or_u32(
                "overriding min aligned length with user-provided value",
                1_u32,
            );

            Ok(AlignmentFilters::builder()
                .five_prime_clip(fpc)
                .three_prime_clip(tpc)
                .score_threshold(st)
                .min_aligned_fraction(maf)
                .min_aligned_len(mal)
                .which_strand(args.strand_filter)
                .model_coverage(args.model_coverage)
                .build())
        }
        Some(FilterGroup::NanocountFilters) => {
            info!("setting filters to nanocount defaults.");
            // override individual parameters if the user passed them in explicitly
            let fpc = args
                .five_prime_clip
                .provided_or_u32("overriding 5' clip with user-provided value", u32::MAX);
            let tpc = args
                .three_prime_clip
                .provided_or_i64("overriding 3' clip with user-provided value", 50_i64);
            let st = args.score_threshold.provided_or_f32(
                "overriding score threshold with user-provided value",
                0.95_f32,
            );
            let maf = args.min_aligned_fraction.provided_or_f32(
                "overriding min aligned fraction with user-provided value",
                0.5_f32,
            );
            let mal = args.min_aligned_len.provided_or_u32(
                "overriding min aligned length with user-provided value",
                50_u32,
            );

            Ok(AlignmentFilters::builder()
                .five_prime_clip(fpc)
                .three_prime_clip(tpc)
                .score_threshold(st)
                .min_aligned_fraction(maf)
                .min_aligned_len(mal)
                .which_strand(bio_types::strand::Strand::Forward)
                .model_coverage(args.model_coverage)
                .build())
        }
        None => {
            info!("setting user-provided filter parameters.");
            Ok(AlignmentFilters::builder()
                .five_prime_clip(args.five_prime_clip.try_as_u32()?)
                .three_prime_clip(args.three_prime_clip.try_as_i64()?)
                .score_threshold(args.score_threshold.try_as_f32()?)
                .min_aligned_fraction(args.min_aligned_fraction.try_as_f32()?)
                .min_aligned_len(args.min_aligned_len.try_as_u32()?)
                .which_strand(args.strand_filter)
                .model_coverage(args.model_coverage)
                .build())
        }
    }
}

fn main() -> anyhow::Result<()> {
    let env_filter = EnvFilter::builder()
        .with_default_directive(LevelFilter::INFO.into())
        .from_env_lossy();
    let (filtered_layer, reload_handle) = tracing_subscriber::reload::Layer::new(env_filter);

    // set up the logging.  Here we will take the
    // logging level from the environment variable if
    // it is set.  Otherwise, we'll set the default
    tracing_subscriber::registry()
        // log level to INFO.
        .with(fmt::layer().with_writer(io::stderr))
        .with(filtered_layer)
        .init();

    let args = Args::parse();

    // change the logging filter if the user specified quiet or
    // verbose.
    if args.quiet {
        reload_handle.modify(|filter| *filter = EnvFilter::new("WARN"))?;
    }
    if args.verbose {
        reload_handle.modify(|filter| *filter = EnvFilter::new("TRACE"))?;
    }

    let filter_opts = get_filter_opts(&args)?;

    let (header, reader, aligner) = if args.alignments.is_none() {
        get_aligner_from_args(&args)?
    } else {
        let alignments = args.alignments.clone().unwrap();
        let afile = File::open(&alignments)?;

        let worker_count = NonZeroUsize::new(1.max(args.threads.saturating_sub(1)))
            .expect("decompression threads >= 1");
        let decoder = bgzf::MultithreadedReader::with_worker_count(worker_count, afile);
        let mut reader = bam::io::Reader::from(decoder);
        // parse the header, and ensure that the reads were mapped with minimap2 (as far as we
        // can tell).
        let header = alignment_parser::read_and_verify_header(&mut reader, &alignments)?;
        (header, Some(reader), None)
    };

    let seqcol_digest = {
        info!("calculating seqcol digest");
        let sc = seqcol_rs::SeqCol::from_sam_header(
            header
                .reference_sequences()
                .iter()
                .map(|(k, v)| (k.as_slice(), v.length().into())),
        );
        let d = sc.digest(seqcol_rs::DigestConfig::default()).context(
            "failed to compute the seqcol digest for the information from the alignment header",
        )?;
        info!("done calculating seqcol digest");
        d
    };
    let num_ref_seqs = header.reference_sequences().len();

    // where we'll write down the per-transcript information we need
    // to track.
    let mut txps: Vec<TranscriptInfo> = Vec::with_capacity(num_ref_seqs);
    let mut txps_name: Vec<String> = Vec::with_capacity(num_ref_seqs);

    // loop over the transcripts in the header and fill in the relevant
    // information here.
    if args.model_coverage {
        for (rseq, rmap) in header.reference_sequences().iter() {
            txps.push(TranscriptInfo::with_len_and_bin_width(
                rmap.length(),
                args.bin_width,
            ));
            txps_name.push(rseq.to_string());
        }
    } else {
        for (rseq, rmap) in header.reference_sequences().iter() {
            txps.push(TranscriptInfo::with_len(rmap.length()));
            txps_name.push(rseq.to_string());
        }
    }
    info!(
        "parsed reference information for {} transcripts.",
        txps.len().to_formatted_string(&Locale::en)
    );

    if args.single_cell {
        // TODO: do this better (quiet the EM during single-cell quant)
        reload_handle.modify(|filter| {
            *filter = if args.quiet {
                EnvFilter::new("WARN")
                    .add_directive("oarfish=warn".parse().unwrap())
                    .add_directive("oarfish::single_cell=warn".parse().unwrap())
            } else if args.verbose {
                EnvFilter::new("TRACE")
                    .add_directive("oarfish=info".parse().unwrap())
                    .add_directive("oarfish::single_cell=trace".parse().unwrap())
            } else {
                // be quiet about normal things in single-cell mode
                // e.g. EM iterations, and only print out info for
                // oarfish::single_cell events.
                EnvFilter::new("INFO")
                    .add_directive("oarfish=warn".parse().unwrap())
                    .add_directive("oarfish::single_cell=info".parse().unwrap())
            }
        })?;

        single_cell::quantify_single_cell_from_collated_bam(
            &header,
            &filter_opts,
            &mut reader.unwrap(),
            &mut txps,
            &args,
            seqcol_digest,
        )?;
    } else if args.alignments.is_some() {
        bulk::quantify_bulk_alignments_from_bam(
            &header,
            filter_opts,
            &mut reader.unwrap(),
            &mut txps,
            &txps_name,
            &args,
            seqcol_digest,
        )?;
    } else {
        bulk::quantify_bulk_alignments_raw_reads(
            &header,
            aligner.expect("need valid alinger to align reads"),
            filter_opts,
            &args.reads.clone().expect("expected read file(s)"),
            &mut txps,
            &txps_name,
            &args,
            seqcol_digest,
        )?;
    }

    Ok(())
}