From 0d6303c593be1e1a8172c78ee6c7c59372289094 Mon Sep 17 00:00:00 2001 From: Evelin Aasna Date: Tue, 12 Sep 2023 13:15:38 +0200 Subject: [PATCH] Update consolidation test data --- .../consolidate/consolidate_matches_test.cpp | 12 +-- .../consolidate/16bins50overlap_dream_all.gff | 46 +++++------ .../16bins50overlap_dream_consolidated.gff | 11 --- .../consolidate/8bins50overlap_dream_all.gff | 28 +++---- .../8bins50overlap_dream_consolidated.gff | 11 --- test/data/consolidate/api_test_input.sh | 35 ++++++++ test/data/consolidate/cli_test_input.sh | 39 --------- test/data/consolidate/cli_test_output.sh | 15 ---- .../{50overlap_full.gff => stellar_truth.gff} | 0 test/data/create_output.sh | 3 - test/data/datasources.cmake | 31 ++------ test/data/dream/cli_test_output.sh | 23 +++--- .../consolidated16bins13window1error.gff | 79 ------------------- .../consolidated16bins15window1error.gff | 79 ------------------- .../dream/consolidated4bins13window1error.gff | 79 ------------------- .../dream/consolidated4bins15window1error.gff | 79 ------------------- test/data/dream/query.fasta | 60 ++++++++++++++ test/data/simulate_input.sh | 2 +- 18 files changed, 154 insertions(+), 478 deletions(-) delete mode 100644 test/data/consolidate/16bins50overlap_dream_consolidated.gff delete mode 100644 test/data/consolidate/8bins50overlap_dream_consolidated.gff create mode 100755 test/data/consolidate/api_test_input.sh delete mode 100755 test/data/consolidate/cli_test_input.sh delete mode 100755 test/data/consolidate/cli_test_output.sh rename test/data/consolidate/{50overlap_full.gff => stellar_truth.gff} (100%) delete mode 100644 test/data/dream/consolidated16bins13window1error.gff delete mode 100644 test/data/dream/consolidated16bins15window1error.gff delete mode 100644 test/data/dream/consolidated4bins13window1error.gff delete mode 100644 test/data/dream/consolidated4bins15window1error.gff create mode 100644 test/data/dream/query.fasta diff --git a/test/api/utilities/consolidate/consolidate_matches_test.cpp b/test/api/utilities/consolidate/consolidate_matches_test.cpp index 53bfa5cf..932df2d4 100644 --- a/test/api/utilities/consolidate/consolidate_matches_test.cpp +++ b/test/api/utilities/consolidate/consolidate_matches_test.cpp @@ -28,14 +28,6 @@ std::filesystem::path consolidation_meta_path(size_t const number_of_bins, size_ return data(name); } -std::filesystem::path stellar_gold_path(size_t const overlap) noexcept -{ - std::string name{}; - name += std::to_string(overlap); - name += "overlap_full.gff"; - return data(name); -} - void compare_gff_out(std::vector const & expected, std::vector const & actual) { @@ -70,7 +62,7 @@ TEST(consolidate_matches, bins8overlap50) valik::consolidate_matches(arguments); valik::database_metadata reference(arguments.ref_meta_path, false); - auto expected = valik::read_stellar_output(stellar_gold_path(segment_overlap), reference, std::ios::binary); + auto expected = valik::read_stellar_output(data("stellar_truth.gff"), reference, std::ios::binary); auto actual = valik::read_stellar_output("consolidated.gff", reference); compare_gff_out(expected, actual); @@ -89,7 +81,7 @@ TEST(consolidate_matches, bins16overlap50) valik::consolidate_matches(arguments); valik::database_metadata reference(arguments.ref_meta_path, false); - auto expected = valik::read_stellar_output(stellar_gold_path(segment_overlap), reference, std::ios::binary); + auto expected = valik::read_stellar_output(data("stellar_truth.gff"), reference, std::ios::binary); auto actual = valik::read_stellar_output("consolidated.gff", reference); compare_gff_out(expected, actual); diff --git a/test/data/consolidate/16bins50overlap_dream_all.gff b/test/data/consolidate/16bins50overlap_dream_all.gff index 489ba607..75408f23 100644 --- a/test/data/consolidate/16bins50overlap_dream_all.gff +++ b/test/data/consolidate/16bins50overlap_dream_all.gff @@ -1,31 +1,31 @@ -3 Stellar eps-matches 1 176 94.382 + . 1;seq2Range=686,863;eValue=5.12253e-72;cigar=169M1I4M1I3M;mutations=49G,57C,71C,89C,97T,165A,170A,173G,175T,176T -3 Stellar eps-matches 1 176 94.382 + . 1;seq2Range=686,863;eValue=5.12253e-72;cigar=169M1I4M1I3M;mutations=49G,57C,71C,89C,97T,165A,170A,173G,175T,176T -3 Stellar eps-matches 1 176 94.382 + . 1;seq2Range=686,863;eValue=5.12253e-72;cigar=169M1I4M1I3M;mutations=49G,57C,71C,89C,97T,165A,170A,173G,175T,176T -2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T -2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T -2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T -2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=3M1I171M1I1M1D9M1D2M1D2M;mutations=4A,46C,63G,96C,105T,135G,168C,176C -2 Stellar eps-matches 148 202 94.7368 + . 1;seq2Range=912,968;eValue=5.69217e-20;cigar=53M1I1M1I1M;mutations=26A,54T,56T -2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T -2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=3M1I171M1I1M1D9M1D2M1D2M;mutations=4A,46C,63G,96C,105T,135G,168C,176C -2 Stellar eps-matches 18 147 94.6153 + . 1;seq2Range=1054,1183;eValue=1.69762e-51;cigar=130M;mutations=2C,14A,24A,35T,41T,54A,65G -2 Stellar eps-matches 148 202 94.7368 + . 1;seq2Range=912,968;eValue=5.69217e-20;cigar=53M1I1M1I1M;mutations=26A,54T,56T -2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=2M1I172M1I1M1D9M1D2M1D2M;mutations=3A,46C,63G,96C,105T,135G,168C,176C -2 Stellar eps-matches 18 147 94.6153 + . 1;seq2Range=1054,1183;eValue=1.69762e-51;cigar=130M;mutations=2C,14A,24A,35T,41T,54A,65G -1 Stellar eps-matches 469 560 94.5652 + . 1;seq2Range=60,151;eValue=7.11652e-35;cigar=92M;mutations=15G,58C,60A,87A,90G -1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G -1 Stellar eps-matches 469 560 94.5652 + . 1;seq2Range=60,151;eValue=7.11652e-35;cigar=92M;mutations=15G,58C,60A,87A,90G -1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I86M2D1M;mutations=54C,70A,84T,94G,109A,139C,150G,163C -1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G +1 Stellar eps-matches 26 205 94.4444 + . 1;seq2Range=1199,1377;eValue=1.33385e-72;cigar=177M1D2M;mutations=2G,42T,56G,61T,107C,120A,137C,169T,172A +1 Stellar eps-matches 72 125 94.4444 + . 1;seq2Range=1640,1693;eValue=2.45585e-18;cigar=54M;mutations=3T,11G,27T 1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I83M2D4M;mutations=54C,70A,84T,94G,109A,139C,150G,163C 1 Stellar eps-matches 126 307 94.0217 + . 1;seq2Range=204,384;eValue=4.05784e-73;cigar=2M1D2M1D171M2I1M1D3M;mutations=19A,24T,96G,159C,166A,170A,176A,177T -1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G +1 Stellar eps-matches 26 205 94.4444 + . 1;seq2Range=1199,1377;eValue=1.33385e-72;cigar=177M1D2M;mutations=2G,42T,56G,61T,107C,120A,137C,169T,172A 1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I83M2D4M;mutations=54C,70A,84T,94G,109A,139C,150G,163C 1 Stellar eps-matches 126 307 94.0217 + . 1;seq2Range=204,384;eValue=4.05784e-73;cigar=2M1D2M1D171M2I1M1D3M;mutations=19A,24T,96G,159C,166A,170A,176A,177T -1 Stellar eps-matches 26 205 94.4444 + . 1;seq2Range=1199,1377;eValue=1.33385e-72;cigar=177M1D2M;mutations=2G,42T,56G,61T,107C,120A,137C,169T,172A +1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G +1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I86M2D1M;mutations=54C,70A,84T,94G,109A,139C,150G,163C +1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G +1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G +1 Stellar eps-matches 469 560 94.5652 + . 1;seq2Range=60,151;eValue=7.11652e-35;cigar=92M;mutations=15G,58C,60A,87A,90G +1 Stellar eps-matches 469 560 94.5652 + . 1;seq2Range=60,151;eValue=7.11652e-35;cigar=92M;mutations=15G,58C,60A,87A,90G 1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I83M2D4M;mutations=54C,70A,84T,94G,109A,139C,150G,163C 1 Stellar eps-matches 126 307 94.0217 + . 1;seq2Range=204,384;eValue=4.05784e-73;cigar=2M1D2M1D171M2I1M1D3M;mutations=19A,24T,96G,159C,166A,170A,176A,177T 1 Stellar eps-matches 26 205 94.4444 + . 1;seq2Range=1199,1377;eValue=1.33385e-72;cigar=177M1D2M;mutations=2G,42T,56G,61T,107C,120A,137C,169T,172A 1 Stellar eps-matches 72 125 94.4444 + . 1;seq2Range=1640,1693;eValue=2.45585e-18;cigar=54M;mutations=3T,11G,27T -1 Stellar eps-matches 26 205 94.4444 + . 1;seq2Range=1199,1377;eValue=1.33385e-72;cigar=177M1D2M;mutations=2G,42T,56G,61T,107C,120A,137C,169T,172A -1 Stellar eps-matches 72 125 94.4444 + . 1;seq2Range=1640,1693;eValue=2.45585e-18;cigar=54M;mutations=3T,11G,27T +2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=2M1I172M1I1M1D9M1D2M1D2M;mutations=3A,46C,63G,96C,105T,135G,168C,176C +2 Stellar eps-matches 18 147 94.6153 + . 1;seq2Range=1054,1183;eValue=1.69762e-51;cigar=130M;mutations=2C,14A,24A,35T,41T,54A,65G +2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T +2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=3M1I171M1I1M1D9M1D2M1D2M;mutations=4A,46C,63G,96C,105T,135G,168C,176C +2 Stellar eps-matches 148 202 94.7368 + . 1;seq2Range=912,968;eValue=5.69217e-20;cigar=53M1I1M1I1M;mutations=26A,54T,56T +2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T +2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T +2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T +2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=3M1I171M1I1M1D9M1D2M1D2M;mutations=4A,46C,63G,96C,105T,135G,168C,176C +2 Stellar eps-matches 18 147 94.6153 + . 1;seq2Range=1054,1183;eValue=1.69762e-51;cigar=130M;mutations=2C,14A,24A,35T,41T,54A,65G +2 Stellar eps-matches 148 202 94.7368 + . 1;seq2Range=912,968;eValue=5.69217e-20;cigar=53M1I1M1I1M;mutations=26A,54T,56T +3 Stellar eps-matches 1 176 94.382 + . 1;seq2Range=686,863;eValue=5.12253e-72;cigar=169M1I4M1I3M;mutations=49G,57C,71C,89C,97T,165A,170A,173G,175T,176T +3 Stellar eps-matches 1 176 94.382 + . 1;seq2Range=686,863;eValue=5.12253e-72;cigar=169M1I4M1I3M;mutations=49G,57C,71C,89C,97T,165A,170A,173G,175T,176T +3 Stellar eps-matches 1 176 94.382 + . 1;seq2Range=686,863;eValue=5.12253e-72;cigar=169M1I4M1I3M;mutations=49G,57C,71C,89C,97T,165A,170A,173G,175T,176T diff --git a/test/data/consolidate/16bins50overlap_dream_consolidated.gff b/test/data/consolidate/16bins50overlap_dream_consolidated.gff deleted file mode 100644 index 99df95a7..00000000 --- a/test/data/consolidate/16bins50overlap_dream_consolidated.gff +++ /dev/null @@ -1,11 +0,0 @@ -3 Stellar eps-matches 1 176 94.382 + . 1;seq2Range=686,863;eValue=5.12253e-72;cigar=169M1I4M1I3M;mutations=49G,57C,71C,89C,97T,165A,170A,173G,175T,176T -2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T -2 Stellar eps-matches 148 202 94.7368 + . 1;seq2Range=912,968;eValue=5.69217e-20;cigar=53M1I1M1I1M;mutations=26A,54T,56T -2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=3M1I171M1I1M1D9M1D2M1D2M;mutations=4A,46C,63G,96C,105T,135G,168C,176C -2 Stellar eps-matches 18 147 94.6153 + . 1;seq2Range=1054,1183;eValue=1.69762e-51;cigar=130M;mutations=2C,14A,24A,35T,41T,54A,65G -1 Stellar eps-matches 469 560 94.5652 + . 1;seq2Range=60,151;eValue=7.11652e-35;cigar=92M;mutations=15G,58C,60A,87A,90G -1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G -1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I83M2D4M;mutations=54C,70A,84T,94G,109A,139C,150G,163C -1 Stellar eps-matches 126 307 94.0217 + . 1;seq2Range=204,384;eValue=4.05784e-73;cigar=2M1D2M1D171M2I1M1D3M;mutations=19A,24T,96G,159C,166A,170A,176A,177T -1 Stellar eps-matches 72 125 94.4444 + . 1;seq2Range=1640,1693;eValue=2.45585e-18;cigar=54M;mutations=3T,11G,27T -1 Stellar eps-matches 26 205 94.4444 + . 1;seq2Range=1199,1377;eValue=1.33385e-72;cigar=177M1D2M;mutations=2G,42T,56G,61T,107C,120A,137C,169T,172A diff --git a/test/data/consolidate/8bins50overlap_dream_all.gff b/test/data/consolidate/8bins50overlap_dream_all.gff index ae92084a..1abc0b5c 100644 --- a/test/data/consolidate/8bins50overlap_dream_all.gff +++ b/test/data/consolidate/8bins50overlap_dream_all.gff @@ -1,20 +1,20 @@ -3 Stellar eps-matches 1 176 94.382 + . 1;seq2Range=686,863;eValue=5.12253e-72;cigar=169M1I4M1I3M;mutations=49G,57C,71C,89C,97T,165A,170A,173G,175T,176T -2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T -2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T -2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=3M1I171M1I1M1D9M1D2M1D2M;mutations=4A,46C,63G,96C,105T,135G,168C,176C -2 Stellar eps-matches 148 202 94.7368 + . 1;seq2Range=912,968;eValue=5.69217e-20;cigar=53M1I1M1I1M;mutations=26A,54T,56T -2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T -2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=2M1I172M1I1M1D9M1D2M1D2M;mutations=3A,46C,63G,96C,105T,135G,168C,176C -2 Stellar eps-matches 18 147 94.6153 + . 1;seq2Range=1054,1183;eValue=1.69762e-51;cigar=130M;mutations=2C,14A,24A,35T,41T,54A,65G -2 Stellar eps-matches 148 202 94.7368 + . 1;seq2Range=912,968;eValue=5.69217e-20;cigar=53M1I1M1I1M;mutations=26A,54T,56T -1 Stellar eps-matches 469 560 94.5652 + . 1;seq2Range=60,151;eValue=7.11652e-35;cigar=92M;mutations=15G,58C,60A,87A,90G -1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I83M2D4M;mutations=54C,70A,84T,94G,109A,139C,150G,163C -1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G 1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I83M2D4M;mutations=54C,70A,84T,94G,109A,139C,150G,163C 1 Stellar eps-matches 126 307 94.0217 + . 1;seq2Range=204,384;eValue=4.05784e-73;cigar=2M1D2M1D171M2I1M1D3M;mutations=19A,24T,96G,159C,166A,170A,176A,177T 1 Stellar eps-matches 26 205 94.4444 + . 1;seq2Range=1199,1377;eValue=1.33385e-72;cigar=177M1D2M;mutations=2G,42T,56G,61T,107C,120A,137C,169T,172A -1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G +1 Stellar eps-matches 72 125 94.4444 + . 1;seq2Range=1640,1693;eValue=2.45585e-18;cigar=54M;mutations=3T,11G,27T 1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I83M2D4M;mutations=54C,70A,84T,94G,109A,139C,150G,163C 1 Stellar eps-matches 126 307 94.0217 + . 1;seq2Range=204,384;eValue=4.05784e-73;cigar=2M1D2M1D171M2I1M1D3M;mutations=19A,24T,96G,159C,166A,170A,176A,177T 1 Stellar eps-matches 26 205 94.4444 + . 1;seq2Range=1199,1377;eValue=1.33385e-72;cigar=177M1D2M;mutations=2G,42T,56G,61T,107C,120A,137C,169T,172A -1 Stellar eps-matches 72 125 94.4444 + . 1;seq2Range=1640,1693;eValue=2.45585e-18;cigar=54M;mutations=3T,11G,27T +1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G +1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I83M2D4M;mutations=54C,70A,84T,94G,109A,139C,150G,163C +1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G +1 Stellar eps-matches 469 560 94.5652 + . 1;seq2Range=60,151;eValue=7.11652e-35;cigar=92M;mutations=15G,58C,60A,87A,90G +2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T +2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=2M1I172M1I1M1D9M1D2M1D2M;mutations=3A,46C,63G,96C,105T,135G,168C,176C +2 Stellar eps-matches 18 147 94.6153 + . 1;seq2Range=1054,1183;eValue=1.69762e-51;cigar=130M;mutations=2C,14A,24A,35T,41T,54A,65G +2 Stellar eps-matches 148 202 94.7368 + . 1;seq2Range=912,968;eValue=5.69217e-20;cigar=53M1I1M1I1M;mutations=26A,54T,56T +2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T +2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=3M1I171M1I1M1D9M1D2M1D2M;mutations=4A,46C,63G,96C,105T,135G,168C,176C +2 Stellar eps-matches 148 202 94.7368 + . 1;seq2Range=912,968;eValue=5.69217e-20;cigar=53M1I1M1I1M;mutations=26A,54T,56T +2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T +3 Stellar eps-matches 1 176 94.382 + . 1;seq2Range=686,863;eValue=5.12253e-72;cigar=169M1I4M1I3M;mutations=49G,57C,71C,89C,97T,165A,170A,173G,175T,176T diff --git a/test/data/consolidate/8bins50overlap_dream_consolidated.gff b/test/data/consolidate/8bins50overlap_dream_consolidated.gff deleted file mode 100644 index 99df95a7..00000000 --- a/test/data/consolidate/8bins50overlap_dream_consolidated.gff +++ /dev/null @@ -1,11 +0,0 @@ -3 Stellar eps-matches 1 176 94.382 + . 1;seq2Range=686,863;eValue=5.12253e-72;cigar=169M1I4M1I3M;mutations=49G,57C,71C,89C,97T,165A,170A,173G,175T,176T -2 Stellar eps-matches 187 386 94.0594 + . 1;seq2Range=662,863;eValue=5.91081e-81;cigar=193M1I4M1I3M;mutations=2T,21C,73G,81C,95C,113C,121T,189A,194A,197G,199T,200T -2 Stellar eps-matches 148 202 94.7368 + . 1;seq2Range=912,968;eValue=5.69217e-20;cigar=53M1I1M1I1M;mutations=26A,54T,56T -2 Stellar eps-matches 68 258 94.3005 + . 1;seq2Range=446,635;eValue=7.45606e-78;cigar=3M1I171M1I1M1D9M1D2M1D2M;mutations=4A,46C,63G,96C,105T,135G,168C,176C -2 Stellar eps-matches 18 147 94.6153 + . 1;seq2Range=1054,1183;eValue=1.69762e-51;cigar=130M;mutations=2C,14A,24A,35T,41T,54A,65G -1 Stellar eps-matches 469 560 94.5652 + . 1;seq2Range=60,151;eValue=7.11652e-35;cigar=92M;mutations=15G,58C,60A,87A,90G -1 Stellar eps-matches 272 426 94.1935 + . 1;seq2Range=2107,2261;eValue=3.12561e-61;cigar=155M;mutations=3A,4G,8A,13A,23C,44C,52C,101C,138G -1 Stellar eps-matches 177 359 94.0217 + . 1;seq2Range=1807,1987;eValue=4.05784e-73;cigar=92M1D1M1I83M2D4M;mutations=54C,70A,84T,94G,109A,139C,150G,163C -1 Stellar eps-matches 126 307 94.0217 + . 1;seq2Range=204,384;eValue=4.05784e-73;cigar=2M1D2M1D171M2I1M1D3M;mutations=19A,24T,96G,159C,166A,170A,176A,177T -1 Stellar eps-matches 72 125 94.4444 + . 1;seq2Range=1640,1693;eValue=2.45585e-18;cigar=54M;mutations=3T,11G,27T -1 Stellar eps-matches 26 205 94.4444 + . 1;seq2Range=1199,1377;eValue=1.33385e-72;cigar=177M1D2M;mutations=2G,42T,56G,61T,107C,120A,137C,169T,172A diff --git a/test/data/consolidate/api_test_input.sh b/test/data/consolidate/api_test_input.sh new file mode 100755 index 00000000..e9abb84d --- /dev/null +++ b/test/data/consolidate/api_test_input.sh @@ -0,0 +1,35 @@ +#!/bin/bash +cd consolidate +set -Eeuo pipefail + +rm -f *_full.gff +rm -f *bins*overlap_segment_metadata.tsv +rm -f *bins*overlap_reference_metadata.tsv + +errRate=0.06 +ref_file=multi_seq_ref.fasta +query_file=query_e${errRate}.fasta +minLen=50 + +stellar -e $errRate -l $minLen -o stellar_truth.gff $ref_file $query_file > /dev/null + +for bin in 8 16 +do + valik split $ref_file --db-meta ${bin}bins${minLen}overlap_reference_metadata.tsv \ + --seg-meta ${bin}bins${minLen}overlap_segment_metadata.tsv \ + --seg-count $bin --overlap $minLen + + while read -r bin_id id start len; + do + end=$(echo $start + $len | bc) + stellar -e $errRate -l $minLen -o multi_seq_ref_${id}_${start}_${len}.gff \ + --sequenceOfInterest $id --segmentBegin $start \ + --segmentEnd $end $ref_file $query_file > /dev/null + + done < ${bin}bins${minLen}overlap_segment_metadata.tsv + + rm ${bin}bins${minLen}overlap_segment_metadata.tsv + + cat multi_seq_ref_*.gff > ${bin}bins${minLen}overlap_dream_all.gff + rm multi_seq_ref_* +done diff --git a/test/data/consolidate/cli_test_input.sh b/test/data/consolidate/cli_test_input.sh deleted file mode 100755 index dcbc3b89..00000000 --- a/test/data/consolidate/cli_test_input.sh +++ /dev/null @@ -1,39 +0,0 @@ -#!/bin/bash -cd consolidate -set -Eeuo pipefail - -# ============================================================ -# Varying error rates -# ============================================================ - -rm -f *_full.gff -rm -f *bins*overlap_segment_metadata.tsv -rm -f *bins*overlap_reference_metadata.tsv - -errRate=0.06 -ref_file=multi_seq_ref.fasta -query_file=query_e${errRate}.fasta - -for minLen in 50 -do - stellar -e $errRate -l $minLen -v -o ${minLen}overlap_full.gff $ref_file $query_file > /dev/null - - for bin in 8 16 - do - valik split $ref_file --db-meta ${bin}bins${minLen}overlap_reference_metadata.tsv \ - --seg-meta ${bin}bins${minLen}overlap_segment_metadata.tsv \ - --seg-count $bin --overlap $minLen - - valik build --from-segments $ref_file --seg-meta ${bin}bins${minLen}overlap_segment_metadata.tsv \ - --ref-meta ${bin}bins${minLen}overlap_reference_metadata.tsv \ - --window 15 --kmer 13 --output ${bin}index.ibf --size 10k - - errors=$(echo "($errRate*$minLen+0.5)/1;" | bc) - valik search --index ${bin}index.ibf --query $query_file --pattern $minLen --error $errors \ - --output ${bin}bins${minLen}overlap_dream_all.gff --ref-meta ${bin}bins${minLen}overlap_reference_metadata.tsv \ - --seg-meta ${bin}bins${minLen}overlap_segment_metadata.tsv - - rm ${bin}index.ibf - rm ${bin}bins${minLen}overlap_segment_metadata.tsv - done -done diff --git a/test/data/consolidate/cli_test_output.sh b/test/data/consolidate/cli_test_output.sh deleted file mode 100755 index 83793540..00000000 --- a/test/data/consolidate/cli_test_output.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash -cd consolidate -set -Eeuo pipefail - -rm -f *_*_dream_consolidated.gff - -for bin in 8 16 -do - for minLen in 50 - do - valik consolidate --input ${bin}bins${minLen}overlap_dream_all.gff \ - --ref-meta ${bin}bins${minLen}overlap_reference_metadata.tsv \ - --output ${bin}bins${minLen}overlap_dream_consolidated.gff - done -done diff --git a/test/data/consolidate/50overlap_full.gff b/test/data/consolidate/stellar_truth.gff similarity index 100% rename from test/data/consolidate/50overlap_full.gff rename to test/data/consolidate/stellar_truth.gff diff --git a/test/data/create_output.sh b/test/data/create_output.sh index fc06b114..d863a2cb 100755 --- a/test/data/create_output.sh +++ b/test/data/create_output.sh @@ -20,9 +20,6 @@ echo "### Running valik build ###" echo "### Running valik search ###" ./search/cli_test_output.sh -echo "### Running valik consolidate ###" -./consolidate/cli_test_output.sh - export VALIK_STELLAR=stellar export VALIK_MERGE=cat diff --git a/test/data/datasources.cmake b/test/data/datasources.cmake index cf444e16..b8f39446 100644 --- a/test/data/datasources.cmake +++ b/test/data/datasources.cmake @@ -182,22 +182,13 @@ declare_datasource (FILE query.fq declare_datasource (FILE 16bins50overlap_dream_all.gff URL ${CMAKE_SOURCE_DIR}/test/data/consolidate/16bins50overlap_dream_all.gff - URL_HASH SHA256=e8f69893d25e86d51399b413a21d6885e4928c3bc1622244c789b30eb4016206) -declare_datasource (FILE 16bins50overlap_dream_consolidated.gff - URL ${CMAKE_SOURCE_DIR}/test/data/consolidate/16bins50overlap_dream_consolidated.gff - URL_HASH SHA256=545709097b8e55a685c132933c3363558c62d4ed1b71892f13de61f35d81c39b) + URL_HASH SHA256=ddb4ae1a76912171d8ab9babf75ffb82dbbd041055b718a89db2d53548079915) declare_datasource (FILE 16bins50overlap_reference_metadata.tsv URL ${CMAKE_SOURCE_DIR}/test/data/consolidate/16bins50overlap_reference_metadata.tsv URL_HASH SHA256=8ed578817aadb6390957047dad4d16e952325e48824d0a7041f6e6a59414ac3d) -declare_datasource (FILE 50overlap_full.gff - URL ${CMAKE_SOURCE_DIR}/test/data/consolidate/50overlap_full.gff - URL_HASH SHA256=45be895caedf69070e3433b5b912f7a20e2ac8ffe227e762fb33e5b31d43106a) declare_datasource (FILE 8bins50overlap_dream_all.gff URL ${CMAKE_SOURCE_DIR}/test/data/consolidate/8bins50overlap_dream_all.gff - URL_HASH SHA256=8786f8b22517bc35b28e3a0406450e6d782a3c47d6ce2ebe4424b1f8a0382fe4) -declare_datasource (FILE 8bins50overlap_dream_consolidated.gff - URL ${CMAKE_SOURCE_DIR}/test/data/consolidate/8bins50overlap_dream_consolidated.gff - URL_HASH SHA256=545709097b8e55a685c132933c3363558c62d4ed1b71892f13de61f35d81c39b) + URL_HASH SHA256=080100b029ec84876c30ec26488ce7b984bf17a01324710c0c85f287866e0fab) declare_datasource (FILE 8bins50overlap_reference_metadata.tsv URL ${CMAKE_SOURCE_DIR}/test/data/consolidate/8bins50overlap_reference_metadata.tsv URL_HASH SHA256=8ed578817aadb6390957047dad4d16e952325e48824d0a7041f6e6a59414ac3d) @@ -207,6 +198,9 @@ declare_datasource (FILE multi_seq_ref.fasta declare_datasource (FILE query_e0.06.fasta URL ${CMAKE_SOURCE_DIR}/test/data/consolidate/query_e0.06.fasta URL_HASH SHA256=b107238db9e0c0515b33fff570a787a86126789a0341bd2fdb52c6c607772f8d) +declare_datasource (FILE stellar_truth.gff + URL ${CMAKE_SOURCE_DIR}/test/data/consolidate/stellar_truth.gff + URL_HASH SHA256=45be895caedf69070e3433b5b912f7a20e2ac8ffe227e762fb33e5b31d43106a) declare_datasource (FILE 16bins13window1error.gff @@ -257,21 +251,12 @@ declare_datasource (FILE 4bins15window1error.gff.preliminary declare_datasource (FILE 4bins15window.ibf URL ${CMAKE_SOURCE_DIR}/test/data/dream/4bins15window.ibf URL_HASH SHA256=8b584d0e55043b3cc0835674dc83f5a7db6143645071f49973a1d085ac4fb919) -declare_datasource (FILE consolidated16bins13window1error.gff - URL ${CMAKE_SOURCE_DIR}/test/data/dream/consolidated16bins13window1error.gff - URL_HASH SHA256=28dc2cffdd32bb8a7bf2a8826280246103a518468bba32e65ec3c121e00c0fde) -declare_datasource (FILE consolidated16bins15window1error.gff - URL ${CMAKE_SOURCE_DIR}/test/data/dream/consolidated16bins15window1error.gff - URL_HASH SHA256=32fbb8e408c436c7876012da039bc91426c18dd47a01d0f48e5b4b78e18da157) -declare_datasource (FILE consolidated4bins13window1error.gff - URL ${CMAKE_SOURCE_DIR}/test/data/dream/consolidated4bins13window1error.gff - URL_HASH SHA256=28dc2cffdd32bb8a7bf2a8826280246103a518468bba32e65ec3c121e00c0fde) -declare_datasource (FILE consolidated4bins15window1error.gff - URL ${CMAKE_SOURCE_DIR}/test/data/dream/consolidated4bins15window1error.gff - URL_HASH SHA256=28dc2cffdd32bb8a7bf2a8826280246103a518468bba32e65ec3c121e00c0fde) declare_datasource (FILE dummy_reads.fastq URL ${CMAKE_SOURCE_DIR}/test/data/dream/dummy_reads.fastq URL_HASH SHA256=f1aa9ca0fb0b87393923848f0389cc3fb5cfd4841566afaf72e6c55829b64d73) +declare_datasource (FILE query.fasta + URL ${CMAKE_SOURCE_DIR}/test/data/dream/query.fasta + URL_HASH SHA256=23ba85ef50015c386b9e23e6f7f63ccc19df89bd9ae09e9a3be4425b7887f106) declare_datasource (FILE query.fastq URL ${CMAKE_SOURCE_DIR}/test/data/dream/query.fastq URL_HASH SHA256=cf44a9c49b3c68f43a2800bf791d215704b50d408fc2ddcdd754d976adb69bea) diff --git a/test/data/dream/cli_test_output.sh b/test/data/dream/cli_test_output.sh index 25c413e5..740ca479 100755 --- a/test/data/dream/cli_test_output.sh +++ b/test/data/dream/cli_test_output.sh @@ -24,6 +24,8 @@ pat_overlap=49 # how much adjacent patterns overlap ref_input="ref.fasta" query="query.fastq" +e=1 +er=$(echo $e/$pattern | bc -l) for b in 4 16 do echo "Splitting the genome into $b segments that overlap by $seg_overlap" @@ -37,22 +39,19 @@ do index=$b"bins"$w"window.ibf" valik build "$ref_input" --kmer "$k" --window "$w" --size "$ibf_size" --output "$index" --from-segments --ref-meta "$ref_meta" --seg-meta "$seg_meta" - for e in 1 - do - echo "Searching IBF with $e errors" - dist_out=$b"bins"$w"window"$e"error.gff" - dist_consolidated="consolidated"$b"bins"$w"window"$e"error.gff" - #local_out="local"$b"bins"$w"window"$e"error.gff" - er=$(echo $e/$pattern | bc -l) - valik search --distribute --index "$index" --query "$query" --output "$dist_out" --error-rate "$er" --pattern "$pattern" --overlap "$pat_overlap" --ref-meta "$ref_meta" --seg-meta "$seg_meta" - #valik search --index "$index" --query "$query" --output "$local_out" --error "$er" --pattern "$pattern" --overlap "$pat_overlap" --ref-meta "$ref_meta" --seg-meta "$seg_meta" - done + echo "Searching IBF with $e errors" + dist_out=$b"bins"$w"window"$e"error.gff" + dist_consolidated="consolidated"$b"bins"$w"window"$e"error.gff" + #local_out="local"$b"bins"$w"window"$e"error.gff" + valik search --distribute --index "$index" --query "$query" --output "$dist_out" --error-rate "$er" --pattern "$pattern" --overlap "$pat_overlap" --ref-meta "$ref_meta" --seg-meta "$seg_meta" + #valik search --index "$index" --query "$query" --output "$local_out" --error "$er" --pattern "$pattern" --overlap "$pat_overlap" --ref-meta "$ref_meta" --seg-meta "$seg_meta" rm $VALIK_TMP/* done done -#stellar_out="stellar.gff" -#stellar ref.fasta query.fasta -e 0.02 -l 50 -o $stellar_out +stellar_out="stellar.gff" +sed -n '1~4s/^@/>/p;2~4p' $query > query.fasta +stellar $ref_input query.fasta -e $er -l $pattern -o $stellar_out rm -r $VALIK_TMP diff --git a/test/data/dream/consolidated16bins13window1error.gff b/test/data/dream/consolidated16bins13window1error.gff deleted file mode 100644 index 8b297838..00000000 --- a/test/data/dream/consolidated16bins13window1error.gff +++ /dev/null @@ -1,79 +0,0 @@ -chr3 Stellar eps-matches 2482 2631 98 - . 9;seq2Range=1,150;cigar=150M;mutations=9C,79G,94G -chr3 Stellar eps-matches 2154 2303 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67T -chr3 Stellar eps-matches 2147 2296 98 + . 3;seq2Range=1,150;cigar=150M;mutations=49T,121A,139G -chr3 Stellar eps-matches 1954 2103 98 - . 6;seq2Range=1,150;cigar=150M;mutations=12C,67G,93G -chr3 Stellar eps-matches 1842 1991 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr3 Stellar eps-matches 1775 1924 98 - . 5;seq2Range=1,150;cigar=150M;mutations=12C,66A,101C -chr3 Stellar eps-matches 1601 1750 98 - . 7;seq2Range=1,150;cigar=150M;mutations=46T,47C,79T -chr3 Stellar eps-matches 1375 1524 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr3 Stellar eps-matches 1141 1290 98 + . 3;seq2Range=1,150;cigar=150M;mutations=19G,49T,67T -chr3 Stellar eps-matches 1128 1277 98 - . 7;seq2Range=1,150;cigar=150M;mutations=45G,67C,124C -chr3 Stellar eps-matches 1125 1274 98 + . 1;seq2Range=2,150;cigar=1M1D148M;mutations=67A,141T -chr3 Stellar eps-matches 1100 1249 98 - . 5;seq2Range=1,150;cigar=150M;mutations=32G,74C,101C -chr3 Stellar eps-matches 1003 1152 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,111G,120T -chr3 Stellar eps-matches 966 1115 98 + . 2;seq2Range=1,150;cigar=150M;mutations=8A,16A,113C -chr3 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr3 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr3 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr3 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr3 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr3 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr3 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr3 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr3 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr3 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr3 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr3 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr3 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr3 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr3 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr3 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr3 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T -chr2 Stellar eps-matches 2170 2300 98.4732 + . 2;seq2Range=17,147;cigar=131M;mutations=7C,51T -chr2 Stellar eps-matches 2147 2296 98 + . 3;seq2Range=1,150;cigar=150M;mutations=49T,121A,139G -chr2 Stellar eps-matches 1954 2103 98 - . 6;seq2Range=1,150;cigar=150M;mutations=12C,67G,93G -chr2 Stellar eps-matches 1842 1991 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr2 Stellar eps-matches 1775 1924 98 - . 5;seq2Range=1,150;cigar=150M;mutations=12C,66A,101C -chr2 Stellar eps-matches 1601 1750 98 - . 7;seq2Range=1,150;cigar=150M;mutations=46T,47C,79T -chr2 Stellar eps-matches 1375 1524 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr2 Stellar eps-matches 1141 1290 98 + . 3;seq2Range=1,150;cigar=150M;mutations=19G,49T,67T -chr2 Stellar eps-matches 1128 1277 98 - . 7;seq2Range=1,150;cigar=150M;mutations=45G,67C,124C -chr2 Stellar eps-matches 1125 1274 98 + . 1;seq2Range=2,150;cigar=1M1D148M;mutations=67A,141T -chr2 Stellar eps-matches 1100 1249 98 - . 5;seq2Range=1,150;cigar=150M;mutations=32G,74C,101C -chr2 Stellar eps-matches 1003 1152 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,111G,120T -chr2 Stellar eps-matches 966 1115 98 + . 2;seq2Range=1,150;cigar=150M;mutations=8A,16A,113C -chr2 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr2 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr2 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr2 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr2 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr2 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr2 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr2 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr2 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr2 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr2 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr2 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr2 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr2 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr2 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr2 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr2 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T -chr1 Stellar eps-matches 974 1023 98 + . 2;seq2Range=9,58;cigar=50M;mutations=8A -chr1 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr1 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr1 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr1 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr1 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr1 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr1 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr1 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr1 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr1 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr1 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr1 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr1 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr1 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr1 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr1 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr1 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T diff --git a/test/data/dream/consolidated16bins15window1error.gff b/test/data/dream/consolidated16bins15window1error.gff deleted file mode 100644 index 0ae62b4c..00000000 --- a/test/data/dream/consolidated16bins15window1error.gff +++ /dev/null @@ -1,79 +0,0 @@ -chr3 Stellar eps-matches 2482 2631 98 - . 9;seq2Range=1,150;cigar=150M;mutations=9C,79G,94G -chr3 Stellar eps-matches 2154 2303 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67T -chr3 Stellar eps-matches 2147 2296 98 + . 3;seq2Range=1,150;cigar=150M;mutations=49T,121A,139G -chr3 Stellar eps-matches 1954 2103 98 - . 6;seq2Range=1,150;cigar=150M;mutations=12C,67G,93G -chr3 Stellar eps-matches 1842 1991 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr3 Stellar eps-matches 1775 1924 98 - . 5;seq2Range=1,150;cigar=150M;mutations=12C,66A,101C -chr3 Stellar eps-matches 1601 1750 98 - . 7;seq2Range=1,150;cigar=150M;mutations=46T,47C,79T -chr3 Stellar eps-matches 1375 1524 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr3 Stellar eps-matches 1141 1290 98 + . 3;seq2Range=1,150;cigar=150M;mutations=19G,49T,67T -chr3 Stellar eps-matches 1128 1277 98 - . 7;seq2Range=1,150;cigar=150M;mutations=45G,67C,124C -chr3 Stellar eps-matches 1125 1274 98 + . 1;seq2Range=2,150;cigar=1M1D148M;mutations=67A,141T -chr3 Stellar eps-matches 1100 1249 98 - . 5;seq2Range=1,150;cigar=150M;mutations=32G,74C,101C -chr3 Stellar eps-matches 1003 1152 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,111G,120T -chr3 Stellar eps-matches 966 1115 98 + . 2;seq2Range=1,150;cigar=150M;mutations=8A,16A,113C -chr3 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr3 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=2M1I147M;mutations=3G,103G,124T -chr3 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr3 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr3 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr3 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr3 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr3 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr3 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr3 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr3 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr3 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr3 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr3 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr3 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr3 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr3 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T -chr2 Stellar eps-matches 2170 2300 98.4732 + . 2;seq2Range=17,147;cigar=131M;mutations=7C,51T -chr2 Stellar eps-matches 2147 2296 98 + . 3;seq2Range=1,150;cigar=150M;mutations=49T,121A,139G -chr2 Stellar eps-matches 1954 2103 98 - . 6;seq2Range=1,150;cigar=150M;mutations=12C,67G,93G -chr2 Stellar eps-matches 1842 1991 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr2 Stellar eps-matches 1775 1924 98 - . 5;seq2Range=1,150;cigar=150M;mutations=12C,66A,101C -chr2 Stellar eps-matches 1601 1750 98 - . 7;seq2Range=1,150;cigar=150M;mutations=46T,47C,79T -chr2 Stellar eps-matches 1375 1524 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr2 Stellar eps-matches 1141 1290 98 + . 3;seq2Range=1,150;cigar=150M;mutations=19G,49T,67T -chr2 Stellar eps-matches 1128 1277 98 - . 7;seq2Range=1,150;cigar=150M;mutations=45G,67C,124C -chr2 Stellar eps-matches 1125 1274 98 + . 1;seq2Range=2,150;cigar=1M1D148M;mutations=67A,141T -chr2 Stellar eps-matches 1100 1249 98 - . 5;seq2Range=1,150;cigar=150M;mutations=32G,74C,101C -chr2 Stellar eps-matches 1003 1152 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,111G,120T -chr2 Stellar eps-matches 966 1115 98 + . 2;seq2Range=1,150;cigar=150M;mutations=8A,16A,113C -chr2 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr2 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr2 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr2 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr2 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr2 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr2 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr2 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr2 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr2 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr2 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr2 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr2 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr2 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr2 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr2 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr2 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T -chr1 Stellar eps-matches 974 1023 98 + . 2;seq2Range=9,58;cigar=50M;mutations=8A -chr1 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr1 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr1 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr1 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr1 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr1 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr1 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr1 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr1 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr1 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr1 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr1 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr1 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr1 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr1 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr1 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr1 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T diff --git a/test/data/dream/consolidated4bins13window1error.gff b/test/data/dream/consolidated4bins13window1error.gff deleted file mode 100644 index 8b297838..00000000 --- a/test/data/dream/consolidated4bins13window1error.gff +++ /dev/null @@ -1,79 +0,0 @@ -chr3 Stellar eps-matches 2482 2631 98 - . 9;seq2Range=1,150;cigar=150M;mutations=9C,79G,94G -chr3 Stellar eps-matches 2154 2303 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67T -chr3 Stellar eps-matches 2147 2296 98 + . 3;seq2Range=1,150;cigar=150M;mutations=49T,121A,139G -chr3 Stellar eps-matches 1954 2103 98 - . 6;seq2Range=1,150;cigar=150M;mutations=12C,67G,93G -chr3 Stellar eps-matches 1842 1991 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr3 Stellar eps-matches 1775 1924 98 - . 5;seq2Range=1,150;cigar=150M;mutations=12C,66A,101C -chr3 Stellar eps-matches 1601 1750 98 - . 7;seq2Range=1,150;cigar=150M;mutations=46T,47C,79T -chr3 Stellar eps-matches 1375 1524 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr3 Stellar eps-matches 1141 1290 98 + . 3;seq2Range=1,150;cigar=150M;mutations=19G,49T,67T -chr3 Stellar eps-matches 1128 1277 98 - . 7;seq2Range=1,150;cigar=150M;mutations=45G,67C,124C -chr3 Stellar eps-matches 1125 1274 98 + . 1;seq2Range=2,150;cigar=1M1D148M;mutations=67A,141T -chr3 Stellar eps-matches 1100 1249 98 - . 5;seq2Range=1,150;cigar=150M;mutations=32G,74C,101C -chr3 Stellar eps-matches 1003 1152 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,111G,120T -chr3 Stellar eps-matches 966 1115 98 + . 2;seq2Range=1,150;cigar=150M;mutations=8A,16A,113C -chr3 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr3 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr3 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr3 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr3 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr3 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr3 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr3 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr3 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr3 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr3 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr3 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr3 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr3 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr3 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr3 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr3 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T -chr2 Stellar eps-matches 2170 2300 98.4732 + . 2;seq2Range=17,147;cigar=131M;mutations=7C,51T -chr2 Stellar eps-matches 2147 2296 98 + . 3;seq2Range=1,150;cigar=150M;mutations=49T,121A,139G -chr2 Stellar eps-matches 1954 2103 98 - . 6;seq2Range=1,150;cigar=150M;mutations=12C,67G,93G -chr2 Stellar eps-matches 1842 1991 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr2 Stellar eps-matches 1775 1924 98 - . 5;seq2Range=1,150;cigar=150M;mutations=12C,66A,101C -chr2 Stellar eps-matches 1601 1750 98 - . 7;seq2Range=1,150;cigar=150M;mutations=46T,47C,79T -chr2 Stellar eps-matches 1375 1524 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr2 Stellar eps-matches 1141 1290 98 + . 3;seq2Range=1,150;cigar=150M;mutations=19G,49T,67T -chr2 Stellar eps-matches 1128 1277 98 - . 7;seq2Range=1,150;cigar=150M;mutations=45G,67C,124C -chr2 Stellar eps-matches 1125 1274 98 + . 1;seq2Range=2,150;cigar=1M1D148M;mutations=67A,141T -chr2 Stellar eps-matches 1100 1249 98 - . 5;seq2Range=1,150;cigar=150M;mutations=32G,74C,101C -chr2 Stellar eps-matches 1003 1152 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,111G,120T -chr2 Stellar eps-matches 966 1115 98 + . 2;seq2Range=1,150;cigar=150M;mutations=8A,16A,113C -chr2 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr2 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr2 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr2 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr2 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr2 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr2 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr2 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr2 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr2 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr2 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr2 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr2 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr2 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr2 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr2 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr2 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T -chr1 Stellar eps-matches 974 1023 98 + . 2;seq2Range=9,58;cigar=50M;mutations=8A -chr1 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr1 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr1 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr1 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr1 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr1 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr1 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr1 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr1 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr1 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr1 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr1 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr1 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr1 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr1 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr1 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr1 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T diff --git a/test/data/dream/consolidated4bins15window1error.gff b/test/data/dream/consolidated4bins15window1error.gff deleted file mode 100644 index 8b297838..00000000 --- a/test/data/dream/consolidated4bins15window1error.gff +++ /dev/null @@ -1,79 +0,0 @@ -chr3 Stellar eps-matches 2482 2631 98 - . 9;seq2Range=1,150;cigar=150M;mutations=9C,79G,94G -chr3 Stellar eps-matches 2154 2303 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67T -chr3 Stellar eps-matches 2147 2296 98 + . 3;seq2Range=1,150;cigar=150M;mutations=49T,121A,139G -chr3 Stellar eps-matches 1954 2103 98 - . 6;seq2Range=1,150;cigar=150M;mutations=12C,67G,93G -chr3 Stellar eps-matches 1842 1991 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr3 Stellar eps-matches 1775 1924 98 - . 5;seq2Range=1,150;cigar=150M;mutations=12C,66A,101C -chr3 Stellar eps-matches 1601 1750 98 - . 7;seq2Range=1,150;cigar=150M;mutations=46T,47C,79T -chr3 Stellar eps-matches 1375 1524 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr3 Stellar eps-matches 1141 1290 98 + . 3;seq2Range=1,150;cigar=150M;mutations=19G,49T,67T -chr3 Stellar eps-matches 1128 1277 98 - . 7;seq2Range=1,150;cigar=150M;mutations=45G,67C,124C -chr3 Stellar eps-matches 1125 1274 98 + . 1;seq2Range=2,150;cigar=1M1D148M;mutations=67A,141T -chr3 Stellar eps-matches 1100 1249 98 - . 5;seq2Range=1,150;cigar=150M;mutations=32G,74C,101C -chr3 Stellar eps-matches 1003 1152 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,111G,120T -chr3 Stellar eps-matches 966 1115 98 + . 2;seq2Range=1,150;cigar=150M;mutations=8A,16A,113C -chr3 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr3 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr3 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr3 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr3 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr3 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr3 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr3 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr3 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr3 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr3 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr3 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr3 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr3 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr3 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr3 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr3 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T -chr2 Stellar eps-matches 2170 2300 98.4732 + . 2;seq2Range=17,147;cigar=131M;mutations=7C,51T -chr2 Stellar eps-matches 2147 2296 98 + . 3;seq2Range=1,150;cigar=150M;mutations=49T,121A,139G -chr2 Stellar eps-matches 1954 2103 98 - . 6;seq2Range=1,150;cigar=150M;mutations=12C,67G,93G -chr2 Stellar eps-matches 1842 1991 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr2 Stellar eps-matches 1775 1924 98 - . 5;seq2Range=1,150;cigar=150M;mutations=12C,66A,101C -chr2 Stellar eps-matches 1601 1750 98 - . 7;seq2Range=1,150;cigar=150M;mutations=46T,47C,79T -chr2 Stellar eps-matches 1375 1524 98 + . 0;seq2Range=1,150;cigar=150M;mutations=87C,113A,136A -chr2 Stellar eps-matches 1141 1290 98 + . 3;seq2Range=1,150;cigar=150M;mutations=19G,49T,67T -chr2 Stellar eps-matches 1128 1277 98 - . 7;seq2Range=1,150;cigar=150M;mutations=45G,67C,124C -chr2 Stellar eps-matches 1125 1274 98 + . 1;seq2Range=2,150;cigar=1M1D148M;mutations=67A,141T -chr2 Stellar eps-matches 1100 1249 98 - . 5;seq2Range=1,150;cigar=150M;mutations=32G,74C,101C -chr2 Stellar eps-matches 1003 1152 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,111G,120T -chr2 Stellar eps-matches 966 1115 98 + . 2;seq2Range=1,150;cigar=150M;mutations=8A,16A,113C -chr2 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr2 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr2 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr2 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr2 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr2 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr2 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr2 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr2 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr2 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr2 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr2 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr2 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr2 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr2 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr2 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr2 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T -chr1 Stellar eps-matches 974 1023 98 + . 2;seq2Range=9,58;cigar=50M;mutations=8A -chr1 Stellar eps-matches 858 1007 98 + . 4;seq2Range=1,150;cigar=150M;mutations=3G,32G,69C -chr1 Stellar eps-matches 841 989 98 + . 1;seq2Range=1,150;cigar=1M1I148M;mutations=2G,103G,124T -chr1 Stellar eps-matches 753 902 98 - . 9;seq2Range=1,150;cigar=150M;mutations=56G,79A,94G -chr1 Stellar eps-matches 654 803 98 + . 2;seq2Range=1,150;cigar=150M;mutations=16G,23C,67A -chr1 Stellar eps-matches 612 761 98 + . 4;seq2Range=1,150;cigar=150M;mutations=69G,74A,92G -chr1 Stellar eps-matches 559 708 98 + . 0;seq2Range=1,150;cigar=150M;mutations=15G,56C,113T -chr1 Stellar eps-matches 556 705 98 - . 7;seq2Range=1,150;cigar=150M;mutations=110G,115G,123T -chr1 Stellar eps-matches 509 658 98 - . 8;seq2Range=1,150;cigar=150M;mutations=46G,110T,119T -chr1 Stellar eps-matches 495 644 98 - . 5;seq2Range=1,150;cigar=150M;mutations=14A,90G,124T -chr1 Stellar eps-matches 283 432 98 + . 3;seq2Range=1,150;cigar=150M;mutations=63C,113A,139G -chr1 Stellar eps-matches 181 330 98 - . 8;seq2Range=1,150;cigar=150M;mutations=53C,61T,111G -chr1 Stellar eps-matches 137 288 98.0263 - . 9;seq2Range=1,150;cigar=2D150M;mutations=111G -chr1 Stellar eps-matches 135 286 98.0263 - . 9;seq2Range=1,150;cigar=150M2D;mutations=111G -chr1 Stellar eps-matches 122 271 98 - . 6;seq2Range=1,150;cigar=150M;mutations=47C,72T,74C -chr1 Stellar eps-matches 94 243 98 + . 4;seq2Range=1,150;cigar=150M;mutations=45A,105C,139C -chr1 Stellar eps-matches 14 163 98 - . 6;seq2Range=1,150;cigar=150M;mutations=72T,87T,90G -chr1 Stellar eps-matches 11 160 98 + . 1;seq2Range=1,150;cigar=150M;mutations=68A,79T,142T diff --git a/test/data/dream/query.fasta b/test/data/dream/query.fasta new file mode 100644 index 00000000..c5be2f1a --- /dev/null +++ b/test/data/dream/query.fasta @@ -0,0 +1,60 @@ +>0 start_position=558,length=150,errors=3,reference_id='chr1',reference_file='chr1.fasta' +TGTTGTGGGAGGCTGGGTCTTAAGCAGCGCGCGAGCTGTGATCCAGGCTACCACGCACATAGTGTATGGAAAGTGATCCAGAGTAGACCCGCGGGGGCCTGACCTAACCTATTTAAGTTGTATCGTGGCTATGAGGGTAGTCGCCGGAGA +>1 start_position=10,length=150,errors=3,reference_id='chr1',reference_file='chr1.fasta' +AGTATGGAAGCATAAGCTCTGCATGCAAAGGTACATCAGATCCTGCGGTTGGGTGCCAACCCAAGTGAGTTCACGGGCTCTTGACAGACATCGGAGGATGGTGCACACTCACTCGACCAGCGCAAAGCACAGGATCTCACGTGCGGACAT +>2 start_position=653,length=150,errors=3,reference_id='chr1',reference_file='chr1.fasta' +GGCCTGACCTAACCTGTATAAGCTGTATCGTGGCTATGAGGGTAGTCGCCGGAGAAAACGTATGCTAACTGATTTTTAAGTCGGCGTGGCGCCGAAGCCGGATCGGTTGTAAGCTAGCCGGGCCTAGGGGTTCACCGTAACGGATTAGTC +>3 start_position=282,length=150,errors=3,reference_id='chr1',reference_file='chr1.fasta' +GCGCATTTCACGCTCTCTACGAATGACCGCAACGATCAAATGGGCGAGAACAACTAATTCCGCTTCATGGGGTTTGTGGATTGTGACACAGCGCGCCCGCTACTGCGGGACGAGAGGACGCCCAATTCTGCCAAGGATGATTTAGGGTGT +>4 start_position=611,length=150,errors=3,reference_id='chr1',reference_file='chr1.fasta' +CGGACATAGTGTATGGAAAGTGATCCAGAGTAGACCCGCGGGGGCCTGACCTAACCTATATAAGTTGTGTCGTAGCTATGAGGGTAGTCGCGGGAGAAAACGTATGCTTACTGATTTTTAAGTCGGCGTGGCGCCGAAGCCGGATCGGTT +>5 reverse,start_position=379,length=150,errors=3,reference_id='chr1',reference_file='chr1.fasta' +CTACTCTGGATCAATTTCCATACACTATGTCCGTGGTAGCCTGGATCACAGCTCGCGCGCTGCTTAAGACCGAGCCTCCCACAACAGGCGTAAGAGGTGTAATGGTTGACCACCCTTTTTCAGTGAGAGTCATACGATTGCGGTGGGGTG +>6 reverse,start_position=752,length=150,errors=3,reference_id='chr1',reference_file='chr1.fasta' +GGCCTAGGGGCTTAAGGGGTGTACCGACAGGATACGTACCGGAGACCCCCGCCGTGTTAGGGGAAGCCAAATGCACGTACAAGCATTCCTCCACGATGACTGACCTAAGAGATGTCCGCCCGTGAGATCCTGTGCTTTGCGCTGGTCGAG +>7 reverse,start_position=318,length=150,errors=3,reference_id='chr1',reference_file='chr1.fasta' +CCGGCGACTACCCTCATAGCCACGATACAACTTATATAGGTTAGGTCAGGCCCCCGCGGGTCTACTCTGGATCACTTTCCATACACTATGTCCGTGGTAGCCTGGATCAGAGCTGGCGCGCTTCTTAAGACCGAGCCTCCCACAACAGGC +>8 reverse,start_position=693,length=150,errors=3,reference_id='chr1',reference_file='chr1.fasta' +CTCGCCCATTTGATCGTTGCGGTCATTCGTAGAGAGCGTGAAATGCGCTATGCTCTTCGGTCCTAGGGGCTTAAGGGGTGTACCGACAGGATACGTACCGGAGACGCCCGGCGTGTTAGGGGAAGCCAAAAGAACGTACAAGCATTCCTC +>9 reverse,start_position=121,length=150,errors=3,reference_id='chr1',reference_file='chr1.fasta' +TACCTGGTAAACAACCACGCCTGCGAAAACAGATGTAGGCCCGCAGCGGAGGGGTGACGACTTGAGTTCTATCAGGAAATCATCGCTGGATTTGAATTTGACTAATCCGTTACGGTGAACCCCTAGGCCCGGCTAGCTTACAACCGATCC +>0 start_position=1374,length=150,errors=3,reference_id='chr2',reference_file='chr2.fasta' +ACGGGAGCCTAGGCAATCCCGACGTCCCGCGTGCTGGATAAAGAAAAGGCCGACTGCGCGAAATGAAGAATCGTCAATTTATTGTTCGCAGCTTTACAGTTCTTCTCCGCGGACGGGCAGAGTGGTTTTAAGACCAGGGTCTATGCACAA +>1 start_position=839,length=150,errors=3,reference_id='chr2',reference_file='chr2.fasta' +AGGTCGTGACCCCTCCGCTGCGGGCCTACATCTGTTTTCGCAGGCGTGGTTGTTTACCAGGTATGGTGCTCATCTCTATTAGTCACGGGCAGCATGGTGTCAGCGAACCGCGCGTCTCCTAATTTCTGGTCTACCGATTTAGCCCCGGCA +>2 start_position=965,length=150,errors=3,reference_id='chr2',reference_file='chr2.fasta' +TGGTCTAACGATTTAACCCCGGCAAATAACTTTGGATTGTGGTTGGAGAGTGCCAGAACTGACGGGCGCTGCCGTGGGGCTCCTAACTAAAAACGCCACGGACCTGGCTAACCTTCGTTGTTGACTATAACATTTGAGGGCGCTTCGGAT +>3 start_position=1140,length=150,errors=3,reference_id='chr2',reference_file='chr2.fasta' +GGGTGGTAAACATAGATTGTATATAGTCAACGACATACACTCATTATTTTGCAATTGCGGCATCTCTACTATGTCTTAATTAGTTTTCCCGGATGGCGAAAACGATCTTACAGGAGAAGCGCTACGCTGGTTTGGAAGACACTTAGTATC +>4 start_position=93,length=150,errors=3,reference_id='chr2',reference_file='chr2.fasta' +ACAGACATCGGAGGATGGTGCACACTCACTCGACCAGCGCAAAGAACAGGATCTCACGGGCGGACATCTCTTAGGTCAGTCATCGTGGAGGAATGCTTGTACGTCCTTTTGGCTTCCCCTAACACGGCGGGCGTCTCCCGTACGTATCCT +>5 reverse,start_position=1051,length=150,errors=3,reference_id='chr2',reference_file='chr2.fasta' +AAGATCGTTTTCGCCATCCGGGAAAACTAATGAAGACATAGTTGAGATGCCGCAATTGCATAATAATGAGTGTCTGTCGTTGACTATATAGAATCTATGTCTACCACCCACATAATACTCTGGCAGTATGGGGAATCCGAAGCGCCCTCA +>6 reverse,start_position=197,length=150,errors=3,reference_id='chr2',reference_file='chr2.fasta' +GCATCGGAGTTCGTGGGAGGGTCCACAGTCTTAACAGGAAGTAGCGATTCTGATCCACGTACCTGCGTAAGGTCTAGCAAGATCCTTAGGCCGATGAGGAAGGTTGTGAGTTTTAAATCCAGGGGTATAACCCCTACTACCACTGCTGCA +>7 reverse,start_position=1023,length=150,errors=3,reference_id='chr2',reference_file='chr2.fasta' +TTCCAAACCAGCGTAGCGCTTCTCCTGTAAGATCGTTTTCGCCAGCCGGGAAAACTAATTAAGACACAGTTGAGATGCCGCAATTGCATAATAATGAGTGTATGTCGTTGACTATATAGAATCCATGTTTACCACCCACATAATACTCTG +>8 reverse,start_position=1642,length=150,errors=3,reference_id='chr2',reference_file='chr2.fasta' +AGGCCCCCGCGGGTCTACTCTGGATCACTTTCCATACACTATGTCGGTGGTAGCCTGGATCACAGCTCGCGCGCTGCTTAAGACCGAGCCTCCCACAACAGGCATAAGATGTGTAATGTTTGACCACCCTTTTTCAGCGAGAGTCATACG +>9 reverse,start_position=2014,length=150,errors=3,reference_id='chr2',reference_file='chr2.fasta' +GCGCTATGTTCTTCGGGCCTAGGGGCTTAAGGGGTGTACCGACAGGATACGTACCGGAGACGCCCGCCGTGTTAGGGGAAGCCAAAAGAACGTACAAGCATTCCTCCACGGTGACTGACCTAAGAGATGTCCGCCCGTGAGATCCTGTGC +>0 start_position=1841,length=150,errors=3,reference_id='chr3',reference_file='chr3.fasta' +GCACTGCATGCTCGGATGGAACTCGGAGATCACCTGGAAAGTCAGTGTCATGCGTGGCGGTTTAGTGTTCGACGTAAGAAAAACCTCGAAGACGGACGAGGTATGCAGACATAGCAGCAGTGGTAGTAGGGGTTAAACCCCTGGATTTAA +>1 start_position=1124,length=150,errors=3,reference_id='chr3',reference_file='chr3.fasta' +TTCCAGAGTATTATGTGGGTGGTAAACATAGATTCTATATAGTCAACGACATACACTCATTATTATGAAATTGCGGCATCTCAACTATGTCTTAATTAGTTTTCCCGGATGGCGAAAACGATCTTACAGGAGAAGCGCTACTCTGGTTTG +>2 start_position=2153,length=150,errors=3,reference_id='chr3',reference_file='chr3.fasta' +AGCTGAGCGGTTCAGGCAGAGTCACTACATCTTATATGTAACCACACTCACATAGTTGTTGGGGGCTAACAGCTAAGGATTCCTGGTCCCTGGCACGGATATAGATCACAATCTGGAATTCCCTCCTAAGTACCCGCCCGGTATTCCCAC +>3 start_position=2146,length=150,errors=3,reference_id='chr3',reference_file='chr3.fasta' +CCTTGAAAGCTGAGCGGTTCAGACAGAGTAACTACATCTTATATGTAATCACACTCACATAGTTGTTGGGGGCAAACAGCTAAGGATTCCTGGTCCCTGGCACGGATATAGATCACAATCAGGAATTCCCTCCTAAGTGCCCGCCCGGTA +>4 start_position=857,length=150,errors=3,reference_id='chr3',reference_file='chr3.fasta' +TGGGGGCCTACATCTGTTTTCGCAGGCGTGGGTGTTTACCAGGTATGGTGCTCATCTCTATTAGTCACCGGCAGCATGGTGTCACCGAACCGCGCGTCTCCTAATATCTGGTCTACCGATTTAGCCCCGGCAAATAACTTTGGATTGTGG +>5 reverse,start_position=1106,length=150,errors=3,reference_id='chr3',reference_file='chr3.fasta' +TTTTTCTTACGCCGAACACTAAACCGCCACGCATGACACTGACTTTCCAGGTGATCTCCGAGTTCAATCCGAGCATGCAGTGCGTCTTTCCAGTGTGAGACGGTCATAACTGTACGGAAAAGGCTTACCTTGATAGATGGGAAGAGTAAC +>6 reverse,start_position=2867,length=150,errors=3,reference_id='chr3',reference_file='chr3.fasta' +GAGATGTCCGCCCGTGAGATCCTGTGCTTTGCGCTGGTCGAGTGAGTGTGCACCATCCTCCGATGTCTGTCTAGCGCCCGTGAACATACGTGGGTTGGCACCCAACCGCAGGATCTGATGTACCTTTGCATGCAGAGCTTATGCTTCCAT +>7 reverse,start_position=1280,length=150,errors=3,reference_id='chr3',reference_file='chr3.fasta' +TCCAGTTAGTGCGCGACACTTTTCCCTGATTGGCAGTTCGGCTTATCACTATTCGTCAAGAATCGGCACATTTGATTCTCCCGCGCCATAAGACTGGGTTTTCCAAGTCTACTATGGAGTAGGTACATCGGAGGTTGTCCGCTCAGCGGG +>8 reverse,start_position=1878,length=150,errors=3,reference_id='chr3',reference_file='chr3.fasta' +TGTTTACCACCCACATAATACTCTGGCAGTATGGGGAATCCGAAGCGCCCTCCAATGTTATAGTCAACAACGAATGTTAGCCAGGTCCGTGGCGTTTTTAGTTAGGAGCCGCACGGCAGTGCCCGTCAGTTCTGGCACTCTCCAACCACA +>9 reverse,start_position=399,length=150,errors=3,reference_id='chr3',reference_file='chr3.fasta' +AACTTCAGCAACACTAATAGGCACCATTGGCAATGCATCGGTGCCCAGACTAGTTTCACTGTGGATCCTGTATCATTCGCCGTCGCGTCAAAAGTCGTTTATAACCGACCCATAACTATGGTGCTTAGACCGGACGACGCCGGGATCAAT diff --git a/test/data/simulate_input.sh b/test/data/simulate_input.sh index dab9acc1..b7ff038a 100755 --- a/test/data/simulate_input.sh +++ b/test/data/simulate_input.sh @@ -41,4 +41,4 @@ done ./dream/cli_test_input.sh $SEED -./consolidate/cli_test_input.sh +./consolidate/api_test_input.sh