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use anyhow::{Result, anyhow, bail};
use clap::{ArgGroup, Args};
use std::path::PathBuf;
trait DefaultMappingParams {
const MAX_EC_CARD: u32;
const MAX_HIT_OCC: u32;
const MAX_HIT_OCC_RECOVER: u32;
const MAX_READ_OCC: u32;
const SKIPPING_STRATEGY: &'static str;
const THRESHOLD: f32;
const BIN_SIZE: u32;
const BIN_OVERLAP: u32;
const BCLEN: u16;
const END_CACHE_CAPACITY: usize;
}
struct DefaultParams;
impl DefaultMappingParams for DefaultParams {
const MAX_EC_CARD: u32 = 4096;
const MAX_HIT_OCC: u32 = 256;
const MAX_HIT_OCC_RECOVER: u32 = 1024;
const MAX_READ_OCC: u32 = 2500;
const SKIPPING_STRATEGY: &'static str = "permissive";
const THRESHOLD: f32 = 0.7;
const BIN_SIZE: u32 = 1000;
const BIN_OVERLAP: u32 = 300;
const BCLEN: u16 = 16;
const END_CACHE_CAPACITY: usize = 5_000_000;
}
fn klen_is_good(s: &str) -> Result<usize> {
let k: usize = s
.parse()
.map_err(|_| anyhow!("`{s}` can't be parsed as a number"))?;
if k > 31 {
bail!("klen = {k} must be <= 31");
} else if (k & 1) == 0 {
bail!("klen = {k} must be odd");
} else {
Ok(k)
}
}
#[derive(Args, Clone, Debug)]
#[command(arg_required_else_help = true)]
#[command(group(
ArgGroup::new("ref-input")
.required(true)
.args(&["ref_seqs", "ref_lists", "ref_dirs"]),
))]
pub(crate) struct BuildOpts {
/// ',' separated list of reference FASTA files
#[arg(short = 's', long, help_heading = "Input", value_delimiter = ',')]
pub ref_seqs: Option<Vec<String>>,
/// ',' separated list of files (each listing input FASTA files)
#[arg(short = 'l', long, help_heading = "Input", value_delimiter = ',')]
pub ref_lists: Option<Vec<String>>,
/// ',' separated list of directories (all FASTA files in each directory will be indexed,
/// but not recursively).
#[arg(short = 'd', long, help_heading = "Input", value_delimiter = ',')]
pub ref_dirs: Option<Vec<String>>,
/// length of k-mer to use, must be <= 31 and odd
#[arg(short, long, help_heading = "Index Construction Parameters", default_value_t = 31, value_parser = klen_is_good)]
pub klen: usize,
/// length of minimizer to use; must be < `klen`
#[arg(
short,
long,
help_heading = "Index Construction Parameters",
default_value_t = 19
)]
pub mlen: usize,
/// number of threads to use
#[arg(short, long, help_heading = "Index Construction Parameters")]
pub threads: usize,
/// output file stem
#[arg(short, long)]
pub output: PathBuf,
/// retain the reduced format GFA files produced by cuttlefish that
/// describe the reference cDBG (the default is to remove these).
#[arg(long, help_heading = "Indexing Details")]
pub keep_intermediate_dbg: bool,
/// working directory where temporary files should be placed.
#[arg(short = 'w', long, help_heading = "Indexing Details", default_value_os_t = PathBuf::from("./workdir.noindex"))]
pub work_dir: PathBuf,
/// overwite an existing index if the output path is the same.
#[arg(long, help_heading = "Indexing Details")]
pub overwrite: bool,
/// skip the construction of the equivalence class lookup table
/// when building the index (not recommended).
#[arg(long, help_heading = "Index Construction Parameters")]
pub no_ec_table: bool,
/// If provided (default is not to clip polyA), then reference sequences
/// ending with polyA tails of length greater than or equal to this value
/// will be clipped.
#[arg(long, help_heading = "Index Construction Parameters")]
pub polya_clip_length: Option<usize>,
/// path to (optional) ',' sparated list of decoy sequences used to insert poison
/// k-mer information into the index.
#[arg(long, value_delimiter = ',')]
pub decoy_paths: Option<Vec<PathBuf>>,
/// index construction seed (seed value passed to SSHash index construction; useful if empty
/// buckets occur).
#[arg(
long = "seed",
help_heading = "Index Construction Parameters",
default_value_t = 1
)]
pub seed: u64,
}
#[derive(Args, Clone, Debug)]
pub(crate) struct MapSCOpts {
/// input index prefix
#[arg(short, long, help_heading = "Input")]
pub index: String,
/// geometry of barcode, umi and read
#[arg(short, long)]
pub geometry: String,
/// path to a ',' separated list of read 1 files
#[arg(
short = '1',
long,
help_heading = "Input",
value_delimiter = ',',
required = true
)]
pub read1: Vec<String>,
/// path to a ',' separated list of read 2 files
#[arg(
short = '2',
long,
help_heading = "Input",
value_delimiter = ',',
required = true
)]
pub read2: Vec<String>,
/// number of threads to use
#[arg(short, long, default_value_t = 16)]
pub threads: usize,
/// path to output directory
#[arg(short, long)]
pub output: PathBuf,
/// do not consider poison k-mers, even if the underlying index contains them.
/// In this case, the mapping results will be identical to those obtained as if
/// no poison table was added to the index.
#[arg(long)]
pub no_poison: bool,
/// apply structural constraints when performing mapping.
#[arg(short = 'c', long)]
pub struct_constraints: bool,
/// the skipping strategy to use for k-mer collection
#[arg(long, default_value = &DefaultParams::SKIPPING_STRATEGY, value_parser = clap::builder::PossibleValuesParser::new(["permissive", "strict"]))]
pub skipping_strategy: String,
/// skip checking of the equivalence classes of k-mers that were too
/// ambiguous to be otherwise considered (passing this flag can speed up
/// mapping slightly, but may reduce specificity).
#[arg(long)]
pub ignore_ambig_hits: bool,
/// includes the positions of each mapped read in the resulting RAD file.
#[arg(long)]
pub with_position: bool,
/// determines the maximum cardinality equivalence class
/// (number of (txp, orientation status) pairs) to examine (cannot be used with
/// --ignore-ambig-hits).
#[arg(
long,
short,
default_value_t = DefaultParams::MAX_EC_CARD,
conflicts_with = "ignore_ambig_hits",
help_heading = "Advanced options"
)]
pub max_ec_card: u32,
/// in the first pass, consider only k-mers having <= --max-hit-occ hits.
#[arg(long, default_value_t = DefaultParams::MAX_HIT_OCC, help_heading = "Advanced options")]
pub max_hit_occ: u32,
/// if all k-mers have > --max-hit-occ hits, then make a second pass and consider k-mers
/// having <= --max-hit-occ-recover hits.
#[arg(long, default_value_t = DefaultParams::MAX_HIT_OCC_RECOVER, help_heading = "Advanced options")]
pub max_hit_occ_recover: u32,
/// reads with more than this number of mappings will not have
/// their mappings reported.
#[arg(long, default_value_t = DefaultParams::MAX_READ_OCC, help_heading = "Advanced options")]
pub max_read_occ: u32,
}
#[derive(Args, Clone, Debug)]
#[command(group(
ArgGroup::new("read_source")
.required(true)
.args(["read1", "reads"])
))]
pub(crate) struct MapBulkOpts {
/// input index prefix
#[arg(short, long, help_heading = "Input")]
pub index: String,
/// path to a comma-separated list of read 1 files
#[arg(
short = '1',
long,
help_heading = "Input",
value_delimiter = ',',
requires = "read2"
)]
pub read1: Option<Vec<String>>,
/// path to a ',' separated list of read 2 files
#[arg(
short = '2',
long,
help_heading = "Input",
value_delimiter = ',',
requires = "read1"
)]
pub read2: Option<Vec<String>>,
/// path to a ',' separated list of read unpaired read files
#[arg(short = 'r', long, help_heading = "Input", value_delimiter = ',', conflicts_with_all = ["read1", "read2"])]
pub reads: Option<Vec<String>>,
/// number of threads to use
#[arg(short, long, default_value_t = 16)]
pub threads: usize,
/// path to output directory
#[arg(short, long)]
pub output: PathBuf,
/// do not consider poison k-mers, even if the underlying index contains them.
/// In this case, the mapping results will be identical to those obtained as if
/// no poison table was added to the index.
#[arg(long)]
pub no_poison: bool,
/// apply structural constraints when performing mapping.
#[arg(short = 'c', long)]
pub struct_constraints: bool,
/// skipping strategy to use for k-mer collection
#[arg(long, default_value = &DefaultParams::SKIPPING_STRATEGY, value_parser = clap::builder::PossibleValuesParser::new(["permissive", "strict"]))]
pub skipping_strategy: String,
/// skip checking of the equivalence classes of k-mers that were too
/// ambiguous to be otherwise considered (passing this flag can speed up
/// mapping slightly, but may reduce specificity).
#[arg(long)]
pub ignore_ambig_hits: bool,
/// determines the maximum cardinality equivalence class
/// (number of (txp, orientation status) pairs) to examine (cannot be used with
/// --ignore-ambig-hits).
#[arg(
long,
short,
default_value_t = DefaultParams::MAX_EC_CARD,
conflicts_with = "ignore_ambig_hits",
help_heading = "Advanced options"
)]
pub max_ec_card: u32,
/// in the first pass, consider only k-mers having <= --max-hit-occ hits.
#[arg(long, default_value_t = DefaultParams::MAX_HIT_OCC, help_heading = "Advanced options")]
pub max_hit_occ: u32,
/// if all k-mers have > --max-hit-occ hits, then make a second pass and consider k-mers
/// having <= --max-hit-occ-recover hits.
#[arg(long, default_value_t = DefaultParams::MAX_HIT_OCC_RECOVER, help_heading = "Advanced options")]
pub max_hit_occ_recover: u32,
/// reads with more than this number of mappings will not have
/// their mappings reported.
#[arg(long, default_value_t = DefaultParams::MAX_READ_OCC, help_heading = "Advanced options")]
pub max_read_occ: u32,
}
#[derive(Args, Clone, Debug)]
pub(crate) struct MapSCAtacOpts {
/// input index prefix
#[arg(short, long, help_heading = "Input")]
pub index: String,
/// path to a ',' separated list of read 1 files
#[arg(
short = '1',
long,
help_heading = "Input",
value_delimiter = ',',
requires = "read2"
)]
pub read1: Option<Vec<String>>,
/// path to a ',' separated list of read 2 files
#[arg(
short = '2',
long,
help_heading = "Input",
value_delimiter = ',',
requires = "read1"
)]
pub read2: Option<Vec<String>>,
#[arg(short = 'r', long, help_heading = "Input", value_delimiter = ',', conflicts_with_all = ["read1", "read2"])]
pub reads: Option<Vec<String>>,
/// path to a ',' separated list of barcode files
#[arg(
short = 'b',
long,
help_heading = "Input",
value_delimiter = ','
)]
pub barcode: Option<Vec<String>>,
/// number of threads to use
#[arg(short, long, default_value_t = 16)]
pub threads: usize,
/// path to output directory
#[arg(short, long)]
pub output: PathBuf,
/// skip checking of the equivalence classes of k-mers that were too
/// ambiguous to be otherwise considered (passing this flag can speed up
/// mapping slightly, but may reduce specificity).
#[arg(long)]
pub ignore_ambig_hits: bool,
/// do not consider poison k-mers, even if the underlying index contains them.
/// In this case, the mapping results will be identical to those obtained as if
/// no poison table was added to the index.
#[arg(long)]
pub no_poison: bool,
/// [DEPRECATED] apply structural constraints when performing mapping.
/// This option is no longer supported and will be ignored.
#[arg(short = 'c', long, hide = true)]
pub struct_constraints: bool,
/// the skipping strategy to use for k-mer collection
#[arg(long, default_value = &DefaultParams::SKIPPING_STRATEGY, value_parser = clap::builder::PossibleValuesParser::new(["permissive", "strict"]))]
pub skipping_strategy: String,
/// [DEPRECATED] output mappings in sam format.
/// This option is no longer supported and will be ignored.
#[arg(long, hide = true)]
pub sam_format: bool,
/// [DEPRECATED] output mappings in bed format.
/// This option is no longer supported and will be ignored.
#[arg(long, hide = true)]
pub bed_format: bool,
/// [DEPRECATED] use chromosomes as color.
/// This option is no longer supported and will be ignored.
#[arg(long, hide = true)]
pub use_chr: bool,
/// threshold to be considered for pseudoalignment, default set to 0.7
#[arg(long, default_value_t = DefaultParams::THRESHOLD)]
pub thr: f32,
/// size of virtual color, default set to 1000
#[arg(long, default_value_t = DefaultParams::BIN_SIZE)]
pub bin_size: u32,
/// size for bin overlap, default set to 300
#[arg(long, default_value_t = DefaultParams::BIN_OVERLAP)]
pub bin_overlap: u32,
/// do not apply Tn5 shift to mapped positions
#[arg(long)]
pub no_tn5_shift: bool,
/// [DEPRECATED] Check if any mapping kmer exist for a mate which is not mapped,
/// but there exists mapping for the other read.
/// This option is no longer supported and will be ignored.
#[arg(long, hide = true)]
pub check_kmer_orphan: bool,
/// determines the maximum cardinality equivalence class
/// (number of (txp, orientation status) pairs) to examine (cannot be used with
/// --ignore-ambig-hits).
#[arg(
long,
short,
default_value_t = DefaultParams::MAX_EC_CARD,
conflicts_with = "ignore_ambig_hits",
help_heading = "Advanced options"
)]
pub max_ec_card: u32,
/// in the first pass, consider only k-mers having <= --max-hit-occ hits.
#[arg(long, default_value_t = DefaultParams::MAX_HIT_OCC, help_heading = "Advanced options")]
pub max_hit_occ: u32,
/// if all k-mers have > --max-hit-occ hits, then make a second pass and consider k-mers
/// having <= --max-hit-occ-recover hits.
#[arg(long, default_value_t = DefaultParams::MAX_HIT_OCC_RECOVER, help_heading = "Advanced options")]
pub max_hit_occ_recover: u32,
/// reads with more than this number of mappings will not have
/// their mappings reported.
#[arg(long, default_value_t = DefaultParams::MAX_READ_OCC, help_heading = "Advanced options")]
pub max_read_occ: u32,
/// the length of the barcode sequence
#[arg(long, default_value_t = DefaultParams::BCLEN, help_heading = "Advanced options")]
pub bclen: u16,
/// the capacity of the cache used to provide fast lookup for k-mers at the ends of unitigs
#[arg(long, default_value_t = DefaultParams::END_CACHE_CAPACITY, help_heading = "Advanced options")]
pub end_cache_capacity: usize,
}