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[test] update link to testdata repo
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@h-2
h-2 committed Nov 26, 2023
1 parent 35fbcb5 commit 01b7d01
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Showing 3 changed files with 346 additions and 152 deletions.
26 changes: 25 additions & 1 deletion test/cli/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -73,4 +73,28 @@ target_use_datasources (search_test FILES db_nucl.fasta.gz
output_tblastn_fm_sensitive.m8
output_tblastn_fm_sensitive.sam
output_tblastx_fm_sensitive.m8
output_tblastx_fm_sensitive.sam)
output_tblastx_fm_sensitive.sam
output_blastn_bs_fm_pairs_default.m8
output_blastn_bs_fm_pairs_default.sam
output_blastn_fm_pairs_default.m8
output_blastn_fm_pairs_default.sam
output_blastp_fm_pairs_default.m8
output_blastp_fm_pairs_default.sam
output_blastx_fm_pairs_default.m8
output_blastx_fm_pairs_default.sam
output_tblastn_fm_pairs_default.m8
output_tblastn_fm_pairs_default.sam
output_tblastx_fm_pairs_default.m8
output_tblastx_fm_pairs_default.sam
output_blastn_bs_fm_pairs_sensitive.m8
output_blastn_bs_fm_pairs_sensitive.sam
output_blastn_fm_pairs_sensitive.m8
output_blastn_fm_pairs_sensitive.sam
output_blastp_fm_pairs_sensitive.m8
output_blastp_fm_pairs_sensitive.sam
output_blastx_fm_pairs_sensitive.m8
output_blastx_fm_pairs_sensitive.sam
output_tblastn_fm_pairs_sensitive.m8
output_tblastn_fm_pairs_sensitive.sam
output_tblastx_fm_pairs_sensitive.m8
output_tblastx_fm_pairs_sensitive.sam)
148 changes: 148 additions & 0 deletions test/cli/search_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -619,6 +619,154 @@ TEST_F(search_test, tblastx_fm_sensitive_sam)
"queries_nucl.fasta.gz", "sensitive", "output_tblastx_fm_sensitive.sam", "sam", "output_tblastx_fm_sensitive.sam");
}

// pairs default mode

TEST_F(search_test, blastn_fm_pairs_default_m8)
{
run_search_test("mkindexn", "db_nucl.fasta.gz", "db_nucl_fm.fasta.gz.lba", "fm", "", "searchn",
"queries_nucl.fasta.gz", "pairs-default", "output_blastn_fm_pairs_default.m8", "m8", "output_blastn_fm_pairs_default.m8");
}

TEST_F(search_test, blastn_fm_pairs_default_sam)
{
run_search_test("mkindexn", "db_nucl.fasta.gz", "db_nucl_fm.fasta.gz.lba", "fm", "", "searchn",
"queries_nucl.fasta.gz", "pairs-default", "output_blastn_fm_pairs_default.sam", "sam", "output_blastn_fm_pairs_default.sam");
}

TEST_F(search_test, blastn_bs_fm_pairs_default_m8)
{
run_search_test("mkindexbs", "db_nucl_bs.fasta.gz", "db_nucl_bs_fm.fasta.gz.lba", "fm", "", "searchbs",
"queries_nucl_bs.fasta.gz", "pairs-default", "output_blastn_bs_fm_pairs_default.m8", "m8", "output_blastn_bs_fm_pairs_default.m8");
}

TEST_F(search_test, blastn_bs_fm_pairs_default_sam)
{
run_search_test("mkindexbs", "db_nucl_bs.fasta.gz", "db_nucl_bs_fm.fasta.gz.lba", "fm", "", "searchbs",
"queries_nucl_bs.fasta.gz", "pairs-default", "output_blastn_bs_fm_pairs_default.sam", "sam", "output_blastn_bs_fm_pairs_default.sam");
}

TEST_F(search_test, blastp_fm_pairs_default_m8)
{
run_search_test("mkindexp", "db_prot.fasta.gz", "db_prot_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_prot.fasta.gz", "pairs-default", "output_blastp_fm_pairs_default.m8", "m8", "output_blastp_fm_pairs_default.m8");
}

TEST_F(search_test, blastp_fm_pairs_default_sam)
{
run_search_test("mkindexp", "db_prot.fasta.gz", "db_prot_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_prot.fasta.gz", "pairs-default", "output_blastp_fm_pairs_default.sam", "sam", "output_blastp_fm_pairs_default.sam");
}

TEST_F(search_test, blastx_fm_pairs_default_m8)
{
run_search_test("mkindexp", "db_prot.fasta.gz", "db_prot_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_nucl.fasta.gz", "pairs-default", "output_blastx_fm_pairs_default.m8", "m8", "output_blastx_fm_pairs_default.m8");
}

TEST_F(search_test, blastx_fm_pairs_default_sam)
{
run_search_test("mkindexp", "db_prot.fasta.gz", "db_prot_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_nucl.fasta.gz", "pairs-default", "output_blastx_fm_pairs_default.sam", "sam", "output_blastx_fm_pairs_default.sam");
}

TEST_F(search_test, tblastn_fm_pairs_default_m8)
{
run_search_test("mkindexp", "db_nucl.fasta.gz", "db_trans_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_prot.fasta.gz", "pairs-default", "output_tblastn_fm_pairs_default.m8", "m8", "output_tblastn_fm_pairs_default.m8");
}

TEST_F(search_test, tblastn_fm_pairs_default_sam)
{
run_search_test("mkindexp", "db_nucl.fasta.gz", "db_trans_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_prot.fasta.gz", "pairs-default", "output_tblastn_fm_pairs_default.sam", "sam", "output_tblastn_fm_pairs_default.sam");
}

TEST_F(search_test, tblastx_fm_pairs_default_m8)
{
run_search_test("mkindexp", "db_nucl.fasta.gz", "db_trans_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_nucl.fasta.gz", "pairs-default", "output_tblastx_fm_pairs_default.m8", "m8", "output_tblastx_fm_pairs_default.m8");
}

TEST_F(search_test, tblastx_fm_pairs_default_sam)
{
run_search_test("mkindexp", "db_nucl.fasta.gz", "db_trans_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_nucl.fasta.gz", "pairs-default", "output_tblastx_fm_pairs_default.sam", "sam", "output_tblastx_fm_pairs_default.sam");
}

// pairs sensitive mode

TEST_F(search_test, blastn_fm_pairs_sensitive_m8)
{
run_search_test("mkindexn", "db_nucl.fasta.gz", "db_nucl_fm.fasta.gz.lba", "fm", "", "searchn",
"queries_nucl.fasta.gz", "pairs-sensitive", "output_blastn_fm_pairs_sensitive.m8", "m8", "output_blastn_fm_pairs_sensitive.m8");
}

TEST_F(search_test, blastn_fm_pairs_sensitive_sam)
{
run_search_test("mkindexn", "db_nucl.fasta.gz", "db_nucl_fm.fasta.gz.lba", "fm", "", "searchn",
"queries_nucl.fasta.gz", "pairs-sensitive", "output_blastn_fm_pairs_sensitive.sam", "sam", "output_blastn_fm_pairs_sensitive.sam");
}

TEST_F(search_test, blastn_bs_fm_pairs_sensitive_m8)
{
run_search_test("mkindexbs", "db_nucl_bs.fasta.gz", "db_nucl_bs_fm.fasta.gz.lba", "fm", "", "searchbs",
"queries_nucl_bs.fasta.gz", "pairs-sensitive", "output_blastn_bs_fm_pairs_sensitive.m8", "m8", "output_blastn_bs_fm_pairs_sensitive.m8");
}

TEST_F(search_test, blastn_bs_fm_pairs_sensitive_sam)
{
run_search_test("mkindexbs", "db_nucl_bs.fasta.gz", "db_nucl_bs_fm.fasta.gz.lba", "fm", "", "searchbs",
"queries_nucl_bs.fasta.gz", "pairs-sensitive", "output_blastn_bs_fm_pairs_sensitive.sam", "sam", "output_blastn_bs_fm_pairs_sensitive.sam");
}

TEST_F(search_test, blastp_fm_pairs_sensitive_m8)
{
run_search_test("mkindexp", "db_prot.fasta.gz", "db_prot_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_prot.fasta.gz", "pairs-sensitive", "output_blastp_fm_pairs_sensitive.m8", "m8", "output_blastp_fm_pairs_sensitive.m8");
}

TEST_F(search_test, blastp_fm_pairs_sensitive_sam)
{
run_search_test("mkindexp", "db_prot.fasta.gz", "db_prot_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_prot.fasta.gz", "pairs-sensitive", "output_blastp_fm_pairs_sensitive.sam", "sam", "output_blastp_fm_pairs_sensitive.sam");
}

TEST_F(search_test, blastx_fm_pairs_sensitive_m8)
{
run_search_test("mkindexp", "db_prot.fasta.gz", "db_prot_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_nucl.fasta.gz", "pairs-sensitive", "output_blastx_fm_pairs_sensitive.m8", "m8", "output_blastx_fm_pairs_sensitive.m8");
}

TEST_F(search_test, blastx_fm_pairs_sensitive_sam)
{
run_search_test("mkindexp", "db_prot.fasta.gz", "db_prot_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_nucl.fasta.gz", "pairs-sensitive", "output_blastx_fm_pairs_sensitive.sam", "sam", "output_blastx_fm_pairs_sensitive.sam");
}

TEST_F(search_test, tblastn_fm_pairs_sensitive_m8)
{
run_search_test("mkindexp", "db_nucl.fasta.gz", "db_trans_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_prot.fasta.gz", "pairs-sensitive", "output_tblastn_fm_pairs_sensitive.m8", "m8", "output_tblastn_fm_pairs_sensitive.m8");
}

TEST_F(search_test, tblastn_fm_pairs_sensitive_sam)
{
run_search_test("mkindexp", "db_nucl.fasta.gz", "db_trans_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_prot.fasta.gz", "pairs-sensitive", "output_tblastn_fm_pairs_sensitive.sam", "sam", "output_tblastn_fm_pairs_sensitive.sam");
}

TEST_F(search_test, tblastx_fm_pairs_sensitive_m8)
{
run_search_test("mkindexp", "db_nucl.fasta.gz", "db_trans_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_nucl.fasta.gz", "pairs-sensitive", "output_tblastx_fm_pairs_sensitive.m8", "m8", "output_tblastx_fm_pairs_sensitive.m8");
}

TEST_F(search_test, tblastx_fm_pairs_sensitive_sam)
{
run_search_test("mkindexp", "db_nucl.fasta.gz", "db_trans_fm.fasta.gz.lba", "fm", "li10", "searchp",
"queries_nucl.fasta.gz", "pairs-sensitive", "output_tblastx_fm_pairs_sensitive.sam", "sam", "output_tblastx_fm_pairs_sensitive.sam");
}

// special options

TEST_F(search_test, lazy_loading)
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