From 05262cd738629067922520ac7225a765d42dc846 Mon Sep 17 00:00:00 2001 From: sarahet Date: Thu, 14 Dec 2023 13:09:28 +0100 Subject: [PATCH 1/2] Allow .fna and .faa fasta extensions --- src/mkindex_options.hpp | 2 +- src/search_options.hpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/mkindex_options.hpp b/src/mkindex_options.hpp index 37e000759..66074b7df 100644 --- a/src/mkindex_options.hpp +++ b/src/mkindex_options.hpp @@ -92,7 +92,7 @@ void parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** ar parser.add_section("Input Options"); - std::vector extensions{"fa", "fq", "fasta", "fastq"}; + std::vector extensions{"fa", "fq", "fasta", "fastq", "fna", "faa"}; #ifdef SEQAN_HAS_ZLIB for (auto const & ext : extensions) extensions.push_back(ext + ".gz"); diff --git a/src/search_options.hpp b/src/search_options.hpp index 5b0835f34..7d7589cfb 100644 --- a/src/search_options.hpp +++ b/src/search_options.hpp @@ -154,7 +154,7 @@ void parseCommandLine(LambdaOptions & options, int argc, char const ** argv) parser.add_section("Input options"); - std::vector extensions{"fa", "fq", "fasta", "fastq"}; + std::vector extensions{"fa", "fq", "fasta", "fastq", "fna", "faa"}; #ifdef SEQAN_HAS_ZLIB for (auto const & ext : extensions) extensions.push_back(ext + ".gz"); From 5665dc2bc2327db661b3111ccff84042a3e36044 Mon Sep 17 00:00:00 2001 From: sarahet Date: Thu, 14 Dec 2023 13:10:33 +0100 Subject: [PATCH 2/2] Remove unused file from test data --- test/data/datasources.cmake | 3 --- 1 file changed, 3 deletions(-) diff --git a/test/data/datasources.cmake b/test/data/datasources.cmake index 9e166a689..2b316a26a 100644 --- a/test/data/datasources.cmake +++ b/test/data/datasources.cmake @@ -191,9 +191,6 @@ declare_datasource (FILE output_blastx_fm_fast.m8 declare_datasource (FILE output_blastx_fm_fast.sam URL ${BASEURL}/output_files/output_blastx_fm_fast.sam URL_HASH SHA256=557394a3c75c2da49d3d15c34f10f1eca2e4a934102cfbe92081df0f704b1828) -declare_datasource (FILE output_blastx_fm_lazy.m8 - URL ${BASEURL}/output_files/output_blastx_fm_lazy.m8 - URL_HASH SHA256=d3bb3a5f101e9deab0b7605b83d3c2ce03270545923a65d10b0c7afb52c324b7) declare_datasource (FILE output_blastx_fm_pairs_default.m8 URL ${BASEURL}/output_files/output_blastx_fm_pairs_default.m8 URL_HASH SHA256=9479d7bb3ca8e53b1d425b70867f0d4aeecd73026596997724f4b1d3458ea16f)