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nice groff
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@Zilong-Li
Zilong-Li committed Dec 24, 2024
1 parent 7b09cf9 commit 44719c8
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Showing 2 changed files with 22 additions and 14 deletions.
5 changes: 5 additions & 0 deletions external/popl/popl.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1262,6 +1262,11 @@ inline std::string GroffOptionPrinter::print(const Attribute& max_attribute) con
throw std::invalid_argument("attribute must be 'optional', 'advanced', or 'default'");

std::stringstream s;
for (const auto& option : option_parser_->options()){
// use groff option as the title
if(option->long_name()=="groff")
s << ".TH " << option->description() << "\n";
}
if (!option_parser_->description().empty())
s << ".SH DESCRIPTION\n.PP\n" << option_parser_->description() << "\n";

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31 changes: 17 additions & 14 deletions src/Cmd.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -16,30 +16,33 @@ Param::Param(int argc, char **argv) {
std::string copyr{"PCA All In One (v" + (std::string)VERSION + ") https://github.com/Zilong-Li/PCAone\n" +
"(C) 2021-2024 Zilong Li GNU General Public License v3\n" +
"\n" +
"Usage: use plink files as input and apply default window-based RSVD method\n" +
" PCAone --bfile plink -n 20 \n\n" +
" use csv file as input and apply the Implicitly Restarted Arnoldi Method\n" +
" PCAone --csv csv.zst --svd 0 \n" +
"Usage: use PLINK files as input and apply default window-based RSVD method:\n" +
" $ PCAone -b plink \n\n" +
" use CSV file as input and apply the Implicitly Restarted Arnoldi Method:\n" +
" $ PCAone -c csv.zst -d 0 \n\n" +
" compute ancestry adjusted LD matrix:\n" +
" $ PCAone -b plink -k 2 -D -o adj \n" +
" $ PCAone -B adj -f adj.mbim --print-r2 -o adj \n" +
"\n"};
OptionParser opts(copyr);
opts.add<Value<std::string>, Attribute::headline>("","PCAone","General options:");
auto help_opt = opts.add<Switch>("h", "help", "print all options including hidden advanced options");
opts.add<Value<double>>("m", "memory", "RAM usage in GB unit for out-of-core mode. default is in-core mode", memory, &memory);
opts.add<Value<uint>>("n", "threads", "the number of threads to be used", threads, &threads);
opts.add<Value<uint>>("v", "verbose", "verbosity level for logs. any level x includes messages for all levels (1...x).\n"
"0: silent. no message on screen;\n"
opts.add<Value<uint>>("v", "verbose", "verbosity level for logs. any level x includes messages for all levels (1...x). Options are\n"
"0: silent, no messages on screen;\n"
"1: concise messages to screen;\n"
"2: more verbose information;\n"
"3: enable debug information."
, verbose, &verbose);
opts.add<Value<std::string>, Attribute::headline>("","PCA","PCA algorithms:");
auto svd_opt = opts.add<Value<uint>>("d", "svd", "SVD method to be applied. default 2 is recommended for big data.\n"
auto svd_opt = opts.add<Value<uint>>("d", "svd", "SVD method to be applied. default 2 is recommended for big data. Options are\n"
"0: the Implicitly Restarted Arnoldi Method (IRAM);\n"
"1: the Yu's single-pass Randomized SVD with power iterations;\n"
"2: the accurate window-based Randomized SVD method (PCAone);\n"
"3: the full Singular Value Decomposition.", 2);
opts.add<Value<uint>>("k", "pc", "top k principal components (PCs) to be calculated", k, &k);
opts.add<Value<uint>>("C", "scale", "do scaling for input file.\n"
opts.add<Value<uint>>("C", "scale", "do scaling for input file. Options are\n"
"0: do just centering;\n"
"1: do log transformation eg. log(x+0.01) for RNA-seq data;\n"
"2: do count per median log transformation (CPMED) for scRNAs.", scale, &scale);
Expand Down Expand Up @@ -82,17 +85,17 @@ Param::Param(int argc, char **argv) {

opts.add<Value<std::string>, Attribute::headline>("","MISC","Misc options:");
opts.add<Value<double>>("", "maf", "exclude variants with MAF lower than this value", maf, &maf);
opts.add<Value<int>>("", "project", "project the new samples onto the existing PCs.\n"
opts.add<Value<int>>("", "project", "project the new samples onto the existing PCs. Options are\n"
"0: disabled;\n"
"1: by multiplying the loadings with mean imputation for missing genotypes;\n"
"2: by solving the least squares system Vx=g. skip sites with missingness;\n"
"3: by Augmentation, Decomposition and Procrusters transformation.\n", project, &project);
opts.add<Value<int>>("", "inbreed", "compute the inbreeding coefficient accounting for population structure.\n"
opts.add<Value<int>>("", "inbreed", "compute the inbreeding coefficient accounting for population structure. Options are\n"
"0: disabled;\n"
"1: compute per-site inbreeding coefficient and HWE test.\n", inbreed, &inbreed);
opts.add<Value<double>>("", "ld-r2", "r2 cutoff for LD-based pruning (usually 0.2).", ld_r2, &ld_r2);
opts.add<Value<uint>>("", "ld-bp", "physical distance threshold in bases for LD (usually 1000000).", ld_bp, &ld_bp);
opts.add<Value<int>>("", "ld-stats", "statistics to calculate LD r2 for pairwise SNPs.\n"
opts.add<Value<int>>("", "ld-stats", "statistics to compute LD R2 for pairwise SNPs. Options are\n"
"0: the ancestry adjusted, i.e. correlation between residuals;\n"
"1: the standard, i.e. correlation between two alleles.\n", ld_stats, &ld_stats);
auto clumpfile = opts.add<Value<std::string>>("", "clump", "assoc-like file with target variants and pvalues for clumping.", "", &clump);
Expand All @@ -101,7 +104,7 @@ Param::Param(int argc, char **argv) {
opts.add<Value<double>>("", "clump-p2", "secondary significance threshold for clumped SNPs.", clump_p2, &clump_p2);
opts.add<Value<double>>("", "clump-r2", "r2 cutoff for LD-based clumping.", clump_r2, &clump_r2);
opts.add<Value<uint>>("", "clump-bp", "physical distance threshold in bases for clumping.", clump_bp, &clump_bp);
opts.add<Switch, Attribute::hidden>("", "groff", "print groff formatted help message.", &groff);
opts.add<Switch, Attribute::hidden>("", "groff", "PCAone 1 \"24 December 2024\" \"PCAone-v"+ std::string(VERSION)+"\" \"Bioinformatics tools\"", &groff);

// collect command line options acutal in effect
ss << (std::string) "PCAone (v" + VERSION + ") https://github.com/Zilong-Li/PCAone\n";
Expand Down Expand Up @@ -204,9 +207,9 @@ Param::Param(int argc, char **argv) {
throw std::invalid_argument("not supporting -m option for PCAngsd with BEAGLE file yet!");
if (bands < 4 || bands % 2 != 0)
throw std::invalid_argument("the -w/--batches must be a power of 2 and the minimun is 4.");

if (svd_t == SvdType::PCAoneAlg2 && !noshuffle) perm = true;

} catch (const popl::invalid_option &e) {
std::cerr << "Invalid Option Exception: " << e.what() << "\n";
std::cerr << "error: ";
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