Stores and manages program arguments for Minimac4. More...

#include <prog_args.hpp>

Inheritance diagram for prog_args:

Collaboration diagram for prog_args:

Public Member Functions
bool	help_is_set () const

bool	version_is_set () const

const std::string &	ref_path () const

const std::string &	tar_path () const

const std::string &	map_path () const

const std::string &	out_path () const

const std::string &	emp_out_path () const

const std::string &	sites_out_path () const

const std::string &	temp_prefix () const

savvy::file::format	out_format () const

std::uint8_t	out_compression () const

const std::vector< std::string > &	fmt_fields () const

const std::unordered_set< std::string > &	sample_ids () const

const savvy::genomic_region &	region () const

std::int64_t	chunk_size () const

std::int64_t	overlap () const

std::int16_t	threads () const

std::size_t	temp_buffer () const

std::size_t	min_block_size () const

std::size_t	max_block_size () const

std::size_t	slope_unit () const

float	decay () const

float	min_r2 () const

float	min_ratio () const

float	prob_threshold () const

float	prob_threshold_s1 () const

float	diff_threshold () const

float	min_recom () const

float	error_param () const

bool	all_typed_sites () const

bool	update_m3vcf () const

bool	compress_reference () const

bool	pass_only () const

bool	fail_min_ratio () const

	prog_args ()
	Construct program arguments parser for minimac4.

bool	parse (int argc, char **argv)
	Parse command-line arguments for minimac4.

Public Member Functions inherited from getopt_wrapper
	getopt_wrapper (std::string usage_str, std::vector< option_with_desc > long_opts)
	Constructs a getopt_wrapper object for parsing command-line options.

void	print_usage (std::ostream &os)
	Prints the program usage and all available options to a stream.

Additional Inherited Members
Protected Attributes inherited from getopt_wrapper
std::vector< option >	long_options_
	Storage of long options for getopt parsing.

std::vector< option_with_desc >	opts_
	Original option definitions with descriptions.

std::string	usage_str_
	Program usage/help string.

std::string	short_opt_string_
	Concatenated short option string.

std::size_t	max_long_opt_length_ = 0
	Maximum long option length.

Detailed Description

Stores and manages program arguments for Minimac4.

This class wraps parsed command-line options and provides typed accessors for downstream modules.

Constructor & Destructor Documentation

◆ prog_args()

prog_args::prog_args ( )

inline

Construct program arguments parser for minimac4.

This constructor initializes the getopt-based argument parser with usage instructions and all supported command-line options for minimac4.

Usage:

minimac4 [opts ...] <reference.msav> <target.{sav,bcf,vcf.gz}>
minimac4 [opts ...] --update-m3vcf <reference.m3vcf.gz>
minimac4 [opts ...] --compress-reference <reference.{sav,bcf,vcf.gz}>

Supported options include:

General:
- --help, -h : Print usage.
- --version, -v : Print version.
Input/Output:
- --output, -o <path> : Output path (default: /dev/stdout).
- --output-format, -O <fmt> : Output format (bcf, sav, vcf.gz, …; default: sav).
- --sites, -s <path> : Output path for sites-only file.
- --empirical-output, -e <path> : Path for empirical dosages.
Reference/Target control:
- --all-typed-sites, -a : Include sites that exist only in target VCF.
- --map, -m <file> : Genetic map file.
- --region, -r <region> : Genomic region to impute.
- --sample-ids <list> / --sample-ids-file <file> : Subset samples from reference panel.
Performance:
- --threads, -t <int> : Number of threads (default: 1).
- --temp-buffer, -b <int> : Number of samples to buffer before writing (default: 200).
- --chunk, -c <bp> : Maximum chunk length in base pairs (default: 20,000,000).
- --overlap, -w <bp> : Size of flanking overlap (default: 3,000,000).
HMM/Imputation parameters:
- --match-error <float> : Match error probability (default: 0.01).
- --min-r2 <float> : Minimum estimated r² for output variants.
- --min-ratio <float> : Minimum target/reference site ratio (default: 1e-4).
- --min-ratio-behavior <skip|fail> : Behavior if ratio not met (default: fail).
- --min-recom <float> : Minimum recombination probability (default: 1e-5).
- --prob-threshold <float> : Probability threshold for template selection.
- --prob-threshold-s1 <float> : Probability threshold in original state space.
- --diff-threshold <float> : Probability diff threshold for template selection.
- --decay <float> : Dosage decay in flanking regions (default: 0, disabled).
Reference compression / conversion:
- --update-m3vcf : Convert M3VCF to MVCF.
- --compress-reference : Compress VCF/BCF/SAV into MVCF.
- --min-block-size <int> : Minimum haplotype block size (default: 10).
- --max-block-size <int> : Maximum haplotype block size (default: 65535).
- --slope-unit <int> : Slope parameter for compression heuristic (default: 10).

Note: Some options are deprecated but retained for backward compatibility (e.g., --allTypedSites, --rsid, --meta, --refHaps, …).

See also: getopt_wrapper

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Member Function Documentation

◆ all_typed_sites()

bool prog_args::all_typed_sites ( ) const

inline

Returns: true if all typed sites should be processed.

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◆ chunk_size()

std::int64_t prog_args::chunk_size ( ) const

inline

Returns: Chunk size in base pairs.

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◆ compress_reference()

bool prog_args::compress_reference ( ) const

inline

Returns: true if reference panel should be compressed.

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◆ decay()

float prog_args::decay ( ) const

inline

Returns: HMM decay parameter.

◆ diff_threshold()

float prog_args::diff_threshold ( ) const

inline

Returns: Likelihood difference threshold.

◆ emp_out_path()

const std::string & prog_args::emp_out_path ( ) const

inline

Returns: Empirical R2 output path.

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◆ error_param()

float prog_args::error_param ( ) const

inline

Returns: Genotyping error parameter.

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◆ fail_min_ratio()

bool prog_args::fail_min_ratio ( ) const

inline

Returns: true if failing on min ratio violation is enabled.

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◆ fmt_fields()

const std::vector< std::string > & prog_args::fmt_fields ( ) const

inline

Returns: FORMAT fields to output.

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◆ help_is_set()

bool prog_args::help_is_set ( ) const

inline

Returns: true if --help flag is set.

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◆ map_path()

const std::string & prog_args::map_path ( ) const

inline

Returns: Genetic map path.

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◆ max_block_size()

std::size_t prog_args::max_block_size ( ) const

inline

Returns: Maximum block size.

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◆ min_block_size()

std::size_t prog_args::min_block_size ( ) const

inline

Returns: Minimum block size.

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◆ min_r2()

float prog_args::min_r2 ( ) const

inline

Returns: Minimum imputation R2 threshold.

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◆ min_ratio()

float prog_args::min_ratio ( ) const

inline

Returns: Minimum haplotype pruning ratio.

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◆ min_recom()

float prog_args::min_recom ( ) const

inline

Returns: Minimum recombination rate.

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◆ out_compression()

std::uint8_t prog_args::out_compression ( ) const

inline

Returns: Compression level for output.

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◆ out_format()

savvy::file::format prog_args::out_format ( ) const

inline

Returns: Output file format.

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◆ out_path()

const std::string & prog_args::out_path ( ) const

inline

Returns: Output file path.

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◆ overlap()

std::int64_t prog_args::overlap ( ) const

inline

Returns: Overlap size in base pairs.

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◆ parse()

bool prog_args::parse	(	int	argc,
		char **	argv )

inline

Parse command-line arguments for minimac4.

This function processes both short and long options (via getopt_long) and positional arguments to configure program execution. It updates internal state variables based on recognized options and validates argument counts.

Behavior:

Parses argc and argv using getopt_long().
Recognizes both short (-o) and long (–output) forms.
Updates internal members (e.g., file paths, numeric thresholds, flags).
Handles deprecated options with warnings and backward-compatible behavior.
Validates required positional arguments (reference and target files).
Automatically assigns temporary prefixes and output paths if not provided.

Command-line structure:

minimac4 [options] <reference.msav> <target.{sav,bcf,vcf.gz}>
minimac4 [options] --update-m3vcf <reference.m3vcf.gz>
minimac4 [options] --compress-reference <reference.{sav,bcf,vcf.gz}>

Return conditions:

Returns true if parsing succeeds (including early exits for –help or –version).
Returns false if:
- An invalid option value is provided,
- An unknown option is encountered,
- The number of positional arguments is invalid.

Side effects:

Writes warnings to std::cerr for deprecated options.
Writes error messages to std::cerr on invalid usage.
Sets defaults for temporary prefix (TMPDIR or /tmp) and output suffixes.
Ensures "HDS" is included in format fields if --empirical-output is requested.

Parameters

argc	Number of command-line arguments.
argv	Array of argument strings.

Returns: true if parsing and validation succeed, false otherwise.

Note

Recognized options include general flags (help, version), I/O control, imputation parameters, and reference compression options.
Deprecated options are retained for backward compatibility, but emit warnings.

See also: getopt_long, prog_args

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◆ pass_only()

bool prog_args::pass_only ( ) const

inline

Returns: true if only PASS variants are kept.

◆ prob_threshold()

float prog_args::prob_threshold ( ) const

inline

Returns: Probability threshold for genotype calls.

◆ prob_threshold_s1()

float prog_args::prob_threshold_s1 ( ) const

inline

Returns: Probability threshold for S1 records.

◆ ref_path()

const std::string & prog_args::ref_path ( ) const

inline

Returns: Reference panel path.

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◆ region()

const savvy::genomic_region & prog_args::region ( ) const

inline

Returns: Genomic region to restrict analysis.

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◆ sample_ids()

const std::unordered_set< std::string > & prog_args::sample_ids ( ) const

inline

Returns: Subset of sample IDs.

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◆ sites_out_path()

const std::string & prog_args::sites_out_path ( ) const

inline

Returns: Sites-only output path.

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◆ slope_unit()

std::size_t prog_args::slope_unit ( ) const

inline

Returns: Slope unit size.

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◆ tar_path()

const std::string & prog_args::tar_path ( ) const

inline

Returns: Target panel path.

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◆ temp_buffer()

std::size_t prog_args::temp_buffer ( ) const

inline

Returns: Temporary buffer size.

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◆ temp_prefix()

const std::string & prog_args::temp_prefix ( ) const

inline

Returns: Prefix for temporary files.

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◆ threads()

std::int16_t prog_args::threads ( ) const

inline

Returns: Number of threads to use.

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◆ update_m3vcf()

bool prog_args::update_m3vcf ( ) const

inline

Returns: true if updating M3VCF reference is enabled.

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◆ version_is_set()

bool prog_args::version_is_set ( ) const

inline

Returns: true if --version flag is set.

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The documentation for this class was generated from the following file:

src/prog_args.hpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ prog_args()

Member Function Documentation

◆ all_typed_sites()

◆ chunk_size()

◆ compress_reference()

◆ decay()

◆ diff_threshold()

◆ emp_out_path()

◆ error_param()

◆ fail_min_ratio()

◆ fmt_fields()

◆ help_is_set()

◆ map_path()

◆ max_block_size()

◆ min_block_size()

◆ min_r2()

◆ min_ratio()

◆ min_recom()

◆ out_compression()

◆ out_format()

◆ out_path()

◆ overlap()

◆ parse()

◆ pass_only()

◆ prob_threshold()

◆ prob_threshold_s1()

◆ ref_path()

◆ region()

◆ sample_ids()

◆ sites_out_path()

◆ slope_unit()

◆ tar_path()

◆ temp_buffer()

◆ temp_prefix()

◆ threads()

◆ update_m3vcf()

◆ version_is_set()