From 6b9ffa0311a9e9c756353e0021d89c3cb5e9690c Mon Sep 17 00:00:00 2001 From: Hannes Hauswedell Date: Sun, 4 Aug 2024 17:52:12 +0100 Subject: [PATCH] [doc] fix documentation for --input-alphabet --- src/search.cpp | 2 +- src/shared_misc.hpp | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/search.cpp b/src/search.cpp index 171724b66..38742cf74 100644 --- a/src/search.cpp +++ b/src/search.cpp @@ -208,7 +208,7 @@ void argConv0(LambdaOptions & options) // query file if (options.qryOrigAlphabet == - AlphabetEnum::DNA4) // means "auto", as dna4 not valid as argument to --query-alphabet + AlphabetEnum::DNA4) // means "auto", as dna4 not valid as argument to --input-alphabet { myPrint(options, 1, "Detecting query alphabet... "); options.qryOrigAlphabet = detectSeqFileAlphabet(options.queryFile); diff --git a/src/shared_misc.hpp b/src/shared_misc.hpp index 7211a6908..573d65e1a 100644 --- a/src/shared_misc.hpp +++ b/src/shared_misc.hpp @@ -94,8 +94,8 @@ inline AlphabetEnum detectSeqFileAlphabet(std::string const & path) else if (all_valid(seq)) { std::cerr << "\nWARNING: You query file was detected as non-standard DNA, but it could be AminoAcid, too.\n" - "To explicitly read as AminoAcid, add '--query-alphabet aminoacid'.\n" - "To ignore and disable this warning, add '--query-alphabet dna5'.\n"; + "To explicitly read as AminoAcid, add '--input-alphabet aminoacid'.\n" + "To ignore and disable this warning, add '--input-alphabet dna5'.\n"; return AlphabetEnum::DNA5; } else if (all_valid(seq))