From ad1b7f47d46fdaafced403498702de602f599f83 Mon Sep 17 00:00:00 2001 From: Jaebeom Kim Date: Sat, 2 Dec 2023 17:43:12 +0900 Subject: [PATCH] make modules under development invisible --- src/metabuli.cpp | 79 +++++++++++++++++++++--------------------------- 1 file changed, 35 insertions(+), 44 deletions(-) diff --git a/src/metabuli.cpp b/src/metabuli.cpp index 55c236dd..b7285d0d 100644 --- a/src/metabuli.cpp +++ b/src/metabuli.cpp @@ -48,15 +48,6 @@ std::vector commands = { " ", CITATION_SPACEPHARER, {{"Directory where the DB will be generated", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}}, - {"updateDB", build, &localPar.build, COMMAND_DB, - "Update database based on the list of FASTA files.", - nullptr, - "Jaebeom Kim ", - " ", - CITATION_SPACEPHARER, - {{"DB directory to be updated", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::empty}, - {"A list of FASTA files", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, - {"Mapping file (accession to tax ID)", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}}}, {"classify", classify, &localPar.classify, COMMAND_MAIN, "Assigning taxonomy label to query reads", nullptr, @@ -67,14 +58,14 @@ std::vector commands = { {"DB dir", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory}, {"out dir", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}, {"job ID", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile}}}, - {"filter", filter, &localPar.filter, COMMAND_MAIN, - "Filtering reads based on the classification result", - nullptr, - "Jaebeom Kim ", - " ", - CITATION_SPACEPHARER, - {{"READ FILE", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC, &DbValidator::flatfile}, - {"FILTER DB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory}}}, + // {"filter", filter, &localPar.filter, COMMAND_MAIN, + // "Filtering reads based on the classification result", + // nullptr, + // "Jaebeom Kim ", + // " ", + // CITATION_SPACEPHARER, + // {{"READ FILE", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC, &DbValidator::flatfile}, + // {"FILTER DB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory}}}, {"grade", grade, &localPar.grade, COMMAND_EXPERT, "Grade the classification result (only for benchmarking)", nullptr, @@ -94,14 +85,14 @@ std::vector commands = { {"List of answer sheets (Query ID 2 tax ID)", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, {"List of assembly accessions of reference sequences", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, {"Taxonomy directory", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC, &DbValidator::directory}}}, - {"seqHeader2TaxId", seqHeader2TaxId, &localPar.seqHeader2TaxId, COMMAND_EXPERT, - "It extracts k-mers from query sequences, and compares them to the target database", - nullptr, - "Jaebeom Kim ", - " ", - CITATION_SPACEPHARER, - {{"read-classification", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, - {"Mapping file (accession to tax ID)", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}}}, + // {"seqHeader2TaxId", seqHeader2TaxId, &localPar.seqHeader2TaxId, COMMAND_EXPERT, + // "It extracts k-mers from query sequences, and compares them to the target database", + // nullptr, + // "Jaebeom Kim ", + // " ", + // CITATION_SPACEPHARER, + // {{"read-classification", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, + // {"Mapping file (accession to tax ID)", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}}}, {"add-to-library", addToLibrary, &localPar.addToLibrary, COMMAND_DATABASE_CREATION, "It bins sequences into files according to their species.", nullptr, @@ -111,16 +102,16 @@ std::vector commands = { {{"List of absolute paths of files to be added. One path per line.", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, {"NCBI style accession2taxid file. It should be consistent to tax dump files.", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, {"DB directory", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory}}}, - {"apply-threshold", applyThreshold, &localPar.applyThreshold, COMMAND_EXPERT, - "Assigning taxonomy label to query reads", - nullptr, - "Jaebeom Kim ", - " ", - CITATION_SPACEPHARER, - {{"Old Results", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, - {"OUT DIR", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory}, - {"JOB ID", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile}, - {"TAXONOMY DIR", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}}, + // {"apply-threshold", applyThreshold, &localPar.applyThreshold, COMMAND_EXPERT, + // "Assigning taxonomy label to query reads", + // nullptr, + // "Jaebeom Kim ", + // " ", + // CITATION_SPACEPHARER, + // {{"Old Results", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, + // {"OUT DIR", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory}, + // {"JOB ID", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile}, + // {"TAXONOMY DIR", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}}, {"binning2report", binning2report, &localPar.binning2report, COMMAND_FORMAT_CONVERSION, "It generates Kraken style report file from binning results", nullptr, @@ -131,15 +122,15 @@ std::vector commands = { {"OUT DIR", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::directory}, {"JOB ID", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile}, {"TAXONOMY DIR", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}}, - {"filter-by-genus", filterByGenus, &localPar.filterByGenus, COMMAND_EXPERT, - "It filters out reads classified as a specific genus", - nullptr, - "Jaebeom Kim ", - " ", - CITATION_SPACEPHARER, - {{"Binning Result", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, - {"Genus list", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile}, - {"TAXONOMY DIR", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}}, + // {"filter-by-genus", filterByGenus, &localPar.filterByGenus, COMMAND_EXPERT, + // "It filters out reads classified as a specific genus", + // nullptr, + // "Jaebeom Kim ", + // " ", + // CITATION_SPACEPHARER, + // {{"Binning Result", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfile}, + // {"Genus list", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile}, + // {"TAXONOMY DIR", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}}, {"mapping2taxon", mapping2taxon, &localPar.mapping2taxon, COMMAND_EXPERT, "It takes a mapping file (multiple targets for each read) and generates a read2taxon file (one target for each read)", nullptr,