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Fasta formats #224

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merged 2 commits into from
Dec 14, 2023
Merged

Fasta formats #224

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05262cd
Allow .fna and .faa fasta extensions
sarahet Dec 14, 2023
5665dc2
Remove unused file from test data
sarahet Dec 14, 2023
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2 changes: 1 addition & 1 deletion src/mkindex_options.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ void parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** ar

parser.add_section("Input Options");

std::vector<std::string> extensions{"fa", "fq", "fasta", "fastq"};
std::vector<std::string> extensions{"fa", "fq", "fasta", "fastq", "fna", "faa"};
#ifdef SEQAN_HAS_ZLIB
for (auto const & ext : extensions)
extensions.push_back(ext + ".gz");
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2 changes: 1 addition & 1 deletion src/search_options.hpp
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Expand Up @@ -154,7 +154,7 @@ void parseCommandLine(LambdaOptions & options, int argc, char const ** argv)

parser.add_section("Input options");

std::vector<std::string> extensions{"fa", "fq", "fasta", "fastq"};
std::vector<std::string> extensions{"fa", "fq", "fasta", "fastq", "fna", "faa"};
#ifdef SEQAN_HAS_ZLIB
for (auto const & ext : extensions)
extensions.push_back(ext + ".gz");
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3 changes: 0 additions & 3 deletions test/data/datasources.cmake
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Expand Up @@ -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)
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