From 7155316a0ae908f5a8af4ab0d49634984aefd48f Mon Sep 17 00:00:00 2001 From: Ruoshi Zhang Date: Wed, 17 Feb 2021 16:22:56 +0100 Subject: [PATCH] Display --tax-fdr parameter in commandline options --- src/commons/LocalParameters.h | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/commons/LocalParameters.h b/src/commons/LocalParameters.h index a0ffc1f..e77fda9 100644 --- a/src/commons/LocalParameters.h +++ b/src/commons/LocalParameters.h @@ -66,7 +66,7 @@ class LocalParameters : public Parameters { PARAM_REVERSE_SETDB(PARAM_REVERSE_SETDB_ID,"--reverse-setdb", "Create reversed setdb", "Create additional setDB with reversed fragments to compute under null [0,1]", typeid(int), (void *) &reverseSetDb, "^[0-1]{1}$"), PARAM_EXTRACTORF_SPACER(PARAM_EXTRACTORF_SPACER_ID,"--extractorf-spacer", "Extract orfs from spacers", "change parameter settings for extractorfs when createsetdb for spacer db [0,1]", typeid(int), (void *) &extractorfsSpacer, "^[0-1]{1}$"), PARAM_FDR_CUTOFF(PARAM_FDR_CUTOFF_ID,"--fdr", "FDR cutoff", "FDR cutoff for filtering matches [0.0, 1.0]", typeid(float), (void *) &fdrCutoff, "^0(\\.[0-9]+)?|1(\\.0+)?$"), - PARAM_TAX_FDR_CUTOFF(PARAM_FDR_CUTOFF_ID,"--tax-fdr", "Taxonomy FDR cutoff", "FDR cutoff for taxonomy report [0.0, 1.0]", typeid(float), (void *) &taxFdrCutoff, "^0(\\.[0-9]+)?|1(\\.0+)?$"), + PARAM_TAX_FDR_CUTOFF(PARAM_TAX_FDR_CUTOFF_ID,"--tax-fdr", "Taxonomy FDR cutoff", "FDR cutoff for taxonomy report [0.0, 1.0]", typeid(float), (void *) &taxFdrCutoff, "^0(\\.[0-9]+)?|1(\\.0+)?$"), PARAM_FORMAT_TYPE(PARAM_FORMAT_TYPE_ID,"--fmt", "Output format", "0: short (only matches)\n1: long (matches and hits)\n2: long with nucleotide alignment", typeid(int), (void *) &formatType, "^[0-2]{1}$"), PARAM_REPORT_PAM(PARAM_REPORT_PAM_ID,"--report-pam", "Report PAM", "Report protospacer adjacent motifs up and downstream of hits [0,1]", typeid(int), (void *) &reportPam, "^[0-1]{1}$"), PARAM_FLANKING_SEQ_LEN(PARAM_FLANKING_SEQ_LEN_ID,"--flanking-seq-len", "Flanking sequence length", "Length of protospacer flanking sequence to extract for possible PAMs scanning", typeid(int), (void *) &flankingSeqLen, "^[0-9]{1}[0-9]*$"), @@ -131,6 +131,7 @@ class LocalParameters : public Parameters { predictmatchworkflow = combineList(searchworkflow, filtermatchbyfdr); predictmatchworkflow = combineList(predictmatchworkflow, summarizeresults); predictmatchworkflow = combineList(predictmatchworkflow, findpam); + predictmatchworkflow.push_back(&PARAM_TAX_FDR_CUTOFF); predictmatchworkflow.push_back(&PARAM_RESTRICT_RANKS_MODE); predictmatchworkflow = combineList(predictmatchworkflow, restrictranks); //predictmatchworkflow.push_back(&PARAM_FDR_CUTOFF); @@ -138,7 +139,7 @@ class LocalParameters : public Parameters { predictmatchworkflow.push_back(&PARAM_DB_OUTPUT); predictmatchworkflow.push_back(&PARAM_REPORT_PAM); predictmatchworkflow.push_back(&PARAM_PERFORM_NUCLALN); - predictmatchworkflow.push_back(&PARAM_TAX_FDR_CUTOFF); + easypredictmatchworkflow.push_back(&PARAM_TAX_MAPPING_FILE); easypredictmatchworkflow.push_back(&PARAM_NCBI_TAX_DUMP);