[TEST] update small error rate edge case test

seqan · Mar 18, 2024 · 147b070 · 147b070
1 parent 98a5257
commit 147b070
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Showing 17 changed files with 117 additions and 68 deletions.
diff --git a/include/stellar/utils/fraction.hpp b/include/stellar/utils/fraction.hpp
@@ -26,7 +26,7 @@ struct fraction
     }
 
     template <typename TDenominator>
-    constexpr explicit fraction(uint32_t const numerator, TDenominator const denominator, std::enable_if_t<std::is_unsigned_v<TDenominator>, int> = 0) :
+    constexpr explicit fraction(difference_t const numerator, TDenominator const denominator, std::enable_if_t<std::is_unsigned_v<TDenominator>, int> = 0) :
         _numerator{numerator},
         _denominator{denominator}
     {
@@ -35,8 +35,8 @@ struct fraction
     }
 
     template <typename TDenominator>
-    constexpr fraction(uint32_t const numerator, TDenominator const denominator, std::enable_if_t<std::is_signed_v<TDenominator>, int> = 0) :
-        fraction{_abs(numerator), static_cast<uint32_t>(_abs(denominator))}
+    constexpr fraction(difference_t const numerator, TDenominator const denominator, std::enable_if_t<std::is_signed_v<TDenominator>, int> = 0) :
+        fraction{_abs(numerator), static_cast<size_t>(_abs(denominator))}
     {
         if (numerator < 0)
             _numerator = -_numerator;
@@ -71,7 +71,7 @@ struct fraction
             };
 
             difference_t numerator = parse_int(float_significand_str);
-            uint32_t denominator{1u};
+            std::size_t denominator = 1u;
             for (std::size_t exponent = float_fraction_str.size(); exponent > 0u; --exponent)
                 denominator *= 10;
 
@@ -112,8 +112,8 @@ struct fraction
             exponent--;
         }
 
-        uint32_t numerator = std::llround(normalized_value);
-        uint32_t denominator = 1;
+        difference_t numerator = std::llround(normalized_value);
+        difference_t denominator = 1;
 
         if (exponent > 0) // normalized_value * 2^exponent
         {
@@ -135,7 +135,7 @@ struct fraction
         return _numerator;
     }
 
-    constexpr uint32_t denominator() const
+    constexpr size_t denominator() const
     {
         return _denominator;
     }
@@ -199,7 +199,7 @@ struct fraction
         };
     }
 
-    constexpr fraction limit_denominator(uint64_t max_denominator=1000000) const
+    constexpr fraction limit_denominator(size_t max_denominator=1000000) const
     {
         // https://stackoverflow.com/questions/17537613/does-python-have-a-function-to-reduce-fractions
         // https://hg.python.org/cpython/file/822c7c0d27d1/Lib/fractions.py#l211
@@ -280,9 +280,9 @@ struct fraction
     // std::abs is not constexpr
     constexpr static auto _abs = [](auto a) { return a < 0 ? -a : a; };
 
-    uint32_t _limiter{1000u};
-    uint32_t _numerator{0u};
-    uint32_t _denominator{1u};
+    uint32_t _limiter{10000u};
+    difference_t _numerator{0u};
+    size_t _denominator{1u};
 };
 
 } // namespace stellar::utils
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -87,7 +87,7 @@ add_library ("${PROJECT_NAME}_interface" INTERFACE)
 target_link_libraries ("${PROJECT_NAME}_interface" INTERFACE seqan3::seqan3)
 target_link_libraries ("${PROJECT_NAME}_interface" INTERFACE sharg::sharg)
 target_include_directories ("${PROJECT_NAME}_interface" INTERFACE ../include)
-target_compile_options ("${PROJECT_NAME}_interface" INTERFACE "-pedantic" "-Wall" "-Wextra")
+target_compile_options ("${PROJECT_NAME}_interface" INTERFACE "-pedantic" "-Wall")
 
 # ----------------------------------------------------------------------------
 # Dependencies

diff --git a/src/stellar3.arg_parser.cpp b/src/stellar3.arg_parser.cpp
@@ -198,7 +198,7 @@ void run_stellar(sharg::parser & parser)
     }
 
     options.outputFormat = options.outputFile.substr(options.outputFile.size() - 3);    // file extension previously validated
-    options.epsilon = stellar::utils::fraction::from_double(options.numEpsilon).limit_denominator();
+    options.epsilon = stellar::utils::fraction::from_double_with_limit(options.numEpsilon, options.minLength).limit_denominator();
 
     if (options.strVerificationMethod == to_string(StellarVerificationMethod{AllLocal{}}))
         options.verificationMethod = StellarVerificationMethod{AllLocal{}};

diff --git a/test/cli/CMakeLists.txt b/test/cli/CMakeLists.txt
@@ -60,7 +60,7 @@ target_use_datasources (stellar_test FILES ref.fasta)
 target_use_datasources (stellar_test FILES multi_seq_ref.fasta)
 target_use_datasources (stellar_test FILES query_e0.fasta)
 target_use_datasources (stellar_test FILES query_e0.05.fasta)
-target_use_datasources (stellar_test FILES query_e0.0009.fasta)
+target_use_datasources (stellar_test FILES query_e0.001.fasta)
 
 target_use_datasources (stellar_test FILES segment_0_0_400_e0.gff)
 target_use_datasources (stellar_test FILES segment_0_500_800_e0.gff)
@@ -92,5 +92,7 @@ target_use_datasources (stellar_test FILES subset_0_1_2_e0.05.stdout)
 
 target_use_datasources (stellar_test FILES er_edge_case_e0.gff)
 target_use_datasources (stellar_test FILES er_edge_case_e0.stdout)
+target_use_datasources (stellar_test FILES er_edge_case_e0.001.gff)
+target_use_datasources (stellar_test FILES er_edge_case_e0.001.stdout)
 target_use_datasources (stellar_test FILES er_edge_case_e0.0009.gff)
 target_use_datasources (stellar_test FILES er_edge_case_e0.0009.stdout)
diff --git a/test/cli/create_gold_standard.sh b/test/cli/create_gold_standard.sh
@@ -3,7 +3,7 @@
 set -ex
 
 # hack to stop seqan.app_tests from complaining about relative paths
-for eps in "e-1" "75e-3" "5e-2" "25e-3" "e-4"
+for eps in "0" "e-1" "75e-3" "5e-2" "25e-3"
 do
     ln -s ../512_simSeq1_$eps.fa gold_standard/512_simSeq1_$eps.fa
     ln -s ../512_simSeq2_$eps.fa gold_standard/512_simSeq2_$eps.fa
@@ -28,7 +28,7 @@ echo "./gold_standard_for.sh reverse protein" >> $com_file
 parallel --jobs 6 < $com_file
 rm $com_file
 
-for eps in "e-1" "75e-3" "5e-2" "25e-3" "e-4"
+for eps in "0" "e-1" "75e-3" "5e-2" "25e-3"
 do
     rm gold_standard/512_simSeq1_$eps.fa
     rm gold_standard/512_simSeq2_$eps.fa

diff --git a/test/cli/generate_dna5_reverse_outputs.sh b/test/cli/generate_dna5_reverse_outputs.sh
@@ -16,6 +16,10 @@ call_stellar_reverse()
     ${STELLAR} -e $1 -l 50 -x 10 -k 7 -n 5000 -s 10000 -r -v -o $2.txt ../../512_simSeq1_$2.fa ../../512_simSeq2_$2.fa > $2.txt.stdout
 }
 
+eps="0"
+errRate=0
+call_stellar_reverse $errRate $eps
+
 eps="e-1"
 errRate=0.1
 call_stellar_reverse $errRate $eps
@@ -32,10 +36,6 @@ eps="25e-3"
 errRate=0.025
 call_stellar_reverse $errRate $eps
 
-eps="e-4"
-errRate=0.0001
-call_stellar_reverse $errRate $eps
-
 # ============================================================
 # Varying minimal lengths
 # ============================================================

diff --git a/test/cli/gold_standard_for.sh b/test/cli/gold_standard_for.sh
@@ -42,6 +42,10 @@ call_stellar()
               $ref_file $query_file > $dir/$2.txt.stdout
 }
 
+eps="0"
+errRate=0
+call_stellar $errRate $eps
+
 eps="e-1"
 errRate=0.1
 call_stellar $errRate $eps
@@ -58,10 +62,6 @@ eps="25e-3"
 errRate=0.025
 call_stellar $errRate $eps
 
-eps="e-4"
-errRate=0.0001
-call_stellar $errRate $eps
-
 # ============================================================
 # Varying minimal lengths
 # ============================================================

diff --git a/test/cli/stellar_test.cpp b/test/cli/stellar_test.cpp
@@ -125,7 +125,7 @@ TEST_P(search_small_error, edge_case)
 
     cli_test_result const result = execute_app("stellar",
                                                data("ref.fasta"),
-                                               data("query_e0.0009.fasta"),
+                                               data("query_e0.001.fasta"),
                                                "-o small_er_out.gff",
                                                "--epsilon ", err_str,
                                                "--minLength 1000",
@@ -153,7 +153,7 @@ TEST_P(search_small_error, edge_case)
 
 INSTANTIATE_TEST_SUITE_P(edge_case_suite,
                          search_small_error,
-                         testing::Values(0.0f, 0.0009f),
+                         testing::Values(0.0f, 0.0009f, 0.001f),
                          [] (testing::TestParamInfo<search_small_error::ParamType> const & info)
                          {
                              std::string name =  "er_edge_case_" + std::to_string((int) std::round(info.param * 10000));

diff --git a/test/data/create_output.sh b/test/data/create_output.sh
@@ -44,7 +44,11 @@ done
 # ZERO ERRORS EDGE CASE
 ############################################################
 minLen=1000
-simulationErrRate=0.0009
-searchErrRate=0
-${STELLAR} -e $searchErrRate -l $minLen -v -o er_edge_case/e$searchErrRate.gff ref.fasta query_e$simulationErrRate.fasta > er_edge_case/e$searchErrRate.stdout
+simulationErrRate=0.001
 ${STELLAR} -e $simulationErrRate -l $minLen -v -o er_edge_case/e$simulationErrRate.gff ref.fasta query_e$simulationErrRate.fasta > er_edge_case/e$simulationErrRate.stdout
+
+for searchErrRate in 0 0.0009
+do 
+   ${STELLAR} -e $searchErrRate -l $minLen -v -o er_edge_case/e$searchErrRate.gff ref.fasta query_e$simulationErrRate.fasta > er_edge_case/e$searchErrRate.stdout
+done
+
diff --git a/test/data/datasources.cmake b/test/data/datasources.cmake
@@ -8,6 +8,9 @@ declare_datasource (FILE multi_seq_ref.fasta
 declare_datasource (FILE query_e0.0009.fasta
                 URL ${CMAKE_SOURCE_DIR}/test/data/query_e0.0009.fasta
                 URL_HASH SHA256=1ad1a3d42c801b6518d23ff193b0002da316a290eedde84c96a2ea27693fdc51)
+declare_datasource (FILE query_e0.001.fasta
+                URL ${CMAKE_SOURCE_DIR}/test/data/query_e0.001.fasta
+                URL_HASH SHA256=5aa1989d674d0c0f23b44d001b22b167117b35ea8d5588270c76809d40e3386e)
 declare_datasource (FILE query_e0.05.fasta
                 URL ${CMAKE_SOURCE_DIR}/test/data/query_e0.05.fasta
                 URL_HASH SHA256=5c055b271113473970757db3e313353906b387a46424a88bc137e7948d10066d)
@@ -115,13 +118,19 @@ declare_datasource (FILE segment_all_e0.stdout
                 URL_HASH SHA256=b9755a5a95e7c7ae98e0b553dfb12b0a2027a985626c1484272d2c572d5fe9bc)
 declare_datasource (FILE er_edge_case_e0.0009.gff
                 URL ${CMAKE_SOURCE_DIR}/test/data/er_edge_case/e0.0009.gff
-                URL_HASH SHA256=ce7648a8aa6496624c491ee899ce1ff8e00abe244383352d1e8425c36c4592fb)
+                URL_HASH SHA256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855)
 declare_datasource (FILE er_edge_case_e0.0009.stdout
                 URL ${CMAKE_SOURCE_DIR}/test/data/er_edge_case/e0.0009.stdout
-                URL_HASH SHA256=5a79eb40971d32c93a7c71a90a9ce7bed24992b261b61f38112d15490a5d6b3d)
+                URL_HASH SHA256=ff67d13e22be4cf67a07e9fa264a04562c557e1dcfba7ac91b03d27e7affa70c)
+declare_datasource (FILE er_edge_case_e0.001.gff
+                URL ${CMAKE_SOURCE_DIR}/test/data/er_edge_case/e0.001.gff
+                URL_HASH SHA256=3c91be74c5473c098e507a6974755cba5f57f3266dc6c507e9c49fd92d9c11e5)
+declare_datasource (FILE er_edge_case_e0.001.stdout
+                URL ${CMAKE_SOURCE_DIR}/test/data/er_edge_case/e0.001.stdout
+                URL_HASH SHA256=ff38ce270a2aeeb86bd6c9a31c2a341a9280ef8483d5c502b355c8250b6d5007)
 declare_datasource (FILE er_edge_case_e0.gff
                 URL ${CMAKE_SOURCE_DIR}/test/data/er_edge_case/e0.gff
                 URL_HASH SHA256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855)
 declare_datasource (FILE er_edge_case_e0.stdout
                 URL ${CMAKE_SOURCE_DIR}/test/data/er_edge_case/e0.stdout
-                URL_HASH SHA256=1a29b22b43675a844353931154ce2f88c195fc04ab073fdc83be16fa19ce5766)
+                URL_HASH SHA256=92030d9313d5e83dc6d3d237db0d9773038ba15660b1706e816e1a2765d02d4c)
diff --git a/test/data/er_edge_case/e0.0009.gff b/test/data/er_edge_case/e0.0009.gff
@@ -1 +0,0 @@
-1	Stellar	eps-matches	544	1693	99.913	+	.	1;seq2Range=1807,2956;eValue=0;cigar=1150M;mutations=865A

diff --git a/test/data/er_edge_case/e0.0009.stdout b/test/data/er_edge_case/e0.0009.stdout
@@ -1,13 +1,13 @@
 I/O options:
   database file   : ref.fasta
-  query file      : query_e0.0009.fasta
+  query file      : query_e0.001.fasta
   alphabet        : dna5
   output file     : er_edge_case/e0.0009.gff
   output format   : gff
 
 User specified parameters:
   minimal match length             : 1000
-  maximal error rate (epsilon)     : 0.0009 = (9/10000)
+  maximal error rate (epsilon)     : 0 = (0/1)
   maximal x-drop                   : 5
   search forward strand            : yes
   search reverse complement        : yes
@@ -18,11 +18,11 @@ User specified parameters:
 
 Calculated parameters:
   k-mer length : 32
-  s^min        : 556
+  s^min        : 1000
   threshold    : 969
-  distance cut : 1032
+  distance cut : 1000
   delta        : 16
-  overlap      : 1
+  overlap      : 0
 
 Loaded 1 query sequence.
 Loaded 1 database sequence.
@@ -34,11 +34,6 @@ Constructing index...
 
 Aligning all query sequences to database sequence...
   1
-    # SWIFT hits      : 1
-    Longest hit       : 1150
-    Avg hit length    : 1150
   1, complement
 
-# Eps-matches     : 1
-Longest eps-match : 1150
-Avg match length  : 1150
+# Eps-matches     : 0
diff --git a/test/data/er_edge_case/e0.001.gff b/test/data/er_edge_case/e0.001.gff
@@ -0,0 +1 @@
+1	Stellar	eps-matches	639	1640	99.9001	+	.	1;seq2Range=1806,2807;eValue=0;cigar=1002M;mutations=754A
diff --git a/test/data/er_edge_case/e0.001.stdout b/test/data/er_edge_case/e0.001.stdout
@@ -0,0 +1,44 @@
+I/O options:
+  database file   : ref.fasta
+  query file      : query_e0.001.fasta
+  alphabet        : dna5
+  output file     : er_edge_case/e0.001.gff
+  output format   : gff
+
+User specified parameters:
+  minimal match length             : 1000
+  maximal error rate (epsilon)     : 0.001 = (1/1000)
+  maximal x-drop                   : 5
+  search forward strand            : yes
+  search reverse complement        : yes
+
+  verification strategy            : exact
+  maximal number of matches        : 50
+  duplicate removal every          : 500
+
+Calculated parameters:
+  k-mer length : 32
+  s^min        : 500
+  threshold    : 937
+  distance cut : 1000
+  delta        : 16
+  overlap      : 1
+
+Loaded 1 query sequence.
+Loaded 1 database sequence.
+
+All matches resulting from your search have an E-value of: 
+        0 or smaller  (match score = 1, error penalty = -2)
+
+Constructing index...
+
+Aligning all query sequences to database sequence...
+  1
+    # SWIFT hits      : 1
+    Longest hit       : 1002
+    Avg hit length    : 1002
+  1, complement
+
+# Eps-matches     : 1
+Longest eps-match : 1002
+Avg match length  : 1002
diff --git a/test/data/er_edge_case/e0.stdout b/test/data/er_edge_case/e0.stdout
@@ -1,6 +1,6 @@
 I/O options:
   database file   : ref.fasta
-  query file      : query_e0.0009.fasta
+  query file      : query_e0.001.fasta
   alphabet        : dna5
   output file     : er_edge_case/e0.gff
   output format   : gff
@@ -34,9 +34,6 @@ Constructing index...
 
 Aligning all query sequences to database sequence...
   1
-    # SWIFT hits      : 1
-    Longest hit       : 1150
-    Avg hit length    : 1150
   1, complement
 
 # Eps-matches     : 0
diff --git a/test/data/query_e0.0009.fasta → test/data/query_e0.001.fasta b/test/data/query_e0.0009.fasta → test/data/query_e0.001.fasta
@@ -21,21 +21,19 @@ TCAGAAAAATGGGAGTTCGGTGGCAACAAAGATTTGCACTACATTAGGAAGCTCTGCGCGGAACTGTTTTCTTAGGGAGA
 TGTCGCATGTGACAACCTTCTCAGCAGCAGCTGCCGTAGAGGAGCGGAATTAACACAGTTCGTCATTGTATACCAGCGTG
 TGTAGGGCGTGGGTTCTCCCTAGTGTGGCACAAAAGGACCAACCGCCTCGCCGAAATTCCATACAAGGGGCTTCGCTGCA
 TTACGGTAAGCTCGAGACCCAGACACTGGAAACTACCGCAGCCTTATCGTGCTACAGCGTGATCACTAGTTAACAGGTGG
-TGAGGTACACCGGAAAAGCGCATCTAGGAAGCAGGTACGGAACTCGTACACCTCTTATGCCTGTTGTGGGAGGCTCGGTC
-TTAAGCAGCGCGCGAGCTGTGATCCAGGCTACCACGGACATAGTGTATGGAAAGTGATCCAGAGTAGACCCGCGGGGGCC
-TGACCTAACCTATATAAGTTGTATCGTGGCTATGAGGGTAGTCGCCGGAGAAAACGTATGCTTACTGATTTTTAAGTCGG
-CGTGGCGCCGAAGCCGGATCGGTTGTAAGCTAGCCGGGCCTAGGGGTTCACCGTAACGGATTAGTCAAATTAAAATCCAG
-CGATGACTTCCTGATAGAACTCAAGTCGTGACCCCTCCGCTGCGGGCCTACATCTGTTTTCGCAGGCGTGGTTGTTTACC
-AGGTATGGTGCTCATCTCTATTAGTCACGGGCAGCATGGTGTCACCGAACCGCGCGTCTCCTAATATCTGGTCTACCGAT
-TTAGCCCCGGCAAATAACTTTGGATTGTGGTTGGAGAGTGCCAGAACTGACGGGCGCTGCCGTGGGGCTCCTAACTAAAA
-ACGCCACGGACCTGGCTAACATTCGTTGTTGACTATAACATTTGAGGGCGCTTCGGATTCCCCATACTGCCAGAGTATTA
-TGTGGGTGGTAAACATAGATTCTATATAGTCAACGACATACACTCATTATTATGCAATTGCGGCATCTCAACTATGTCTT
-AATTAGTTTTCCCGGATGGCGAAAACGATCTTACAGGAGAAGCGCTACGCTGGTTTGGAAGACACTTAGTATCCTAGTAG
-TATGGGCTTGTGCGGGTCAACGGGCGCCGTCAAAGCGCACACATATCTGGTGGGGACGGTGTCCCCTATCGGCGCACACG
-GGAGCCTAGGCAATCCCGACGTCCCGCGTGATGGATAAAGAAAAGGCCGACTGCGCGAAATGAAGAATCGTCAATTTATT
-GTTGGCAGCTTTACAGTTCTTCTCCGCGGGCGGGCAGAGTGGTTTTAAGACCGGGGTCTATGCACAAGGGTGGAGCTTGA
-TTACTATCATCGAAGGGTGACTTGCCGTGTTACAATCGACAAGCGAACGGCCGACTGCTTCGGCCCGCTGAGCGGACAAC
-CTCCGATGTACCTACTCCATAGTAGACTTGGAAAACCCAGTCTTATGGCGCGGGGGAATCAAATGTGCCGATTCTTTGGC
-TCGGGTCGATAATCACTATGCTCGTTAATCGTGCCATCCACTGCCCGCTTTAATCCCAACCGGCGTTTCTGCTACATGCT
-AGTCACGAAGGGGCGCCAGGGGATAGGCGAAAGCACTGGCTACGTCATCCTTGCAATAAAAACCGTTGCCTGGCACGGTC
-ATCAAGTATCTCGCGTCGCCCAGTGGCCCC
+TGAGGTACACCGGAAAAGCGCATCTAGGAAGCAGGTACGGAACTCGAGTAGACCCGCGGGGGCCTGACCTAACCTATATA
+AGTTGTATCGTGGCTATGAGGGTAGTCGCCGGAGAAAACGTATGCTTACTGATTTTTAAGTCGGCGTGGCGCCGAAGCCG
+GATCGGTTGTAAGCTAGCCGGGCCTAGGGGTTCACCGTAACGGATTAGTCAAATTAAAATCCAGCGATGACTTCCTGATA
+GAACTCAAGTCGTGACCCCTCCGCTGCGGGCCTACATCTGTTTTCGCAGGCGTGGTTGTTTACCAGGTATGGTGCTCATC
+TCTATTAGTCACGGGCAGCATGGTGTCACCGAACCGCGCGTCTCCTAATATCTGGTCTACCGATTTAGCCCCGGCAAATA
+ACTTTGGATTGTGGTTGGAGAGTGCCAGAACTGACGGGCGCTGCCGTGGGGCTCCTAACTAAAAACGCCACGGACCTGGC
+TAACATTCGTTGTTGACTATAACATTTGAGGGCGCTTCGGATTCCCCATACTGCCAGAGTATTATGTGGGTGGTAAACAT
+AGATTCTATATAGTCAACGACATACACTCATTATTATGCAATTGCGGCATCTCAACTATGTCTTAATTAGTTTTCCCGGA
+TGGCGAAAACGATCTTACAGGAGAAGCGCTACGCTGGTTTGGAAGACACTTAGTATCCTAGTAGTATGGGCTTGTGCGGG
+TCAACGGGCGCCGTCAAAGCGCACACATATCTGGTGGGGACGGTGTCCCCTATCGGCGCACACGGGAGCCTAGGCAATAC
+CGACGTCCCGCGTGCTGGATAAAGAAAAGGCCGACTGCGCGAAATGAAGAATCGTCAATTTATTGTTGGCAGCTTTACAG
+TTCTTCTCCGCGGGCGGGCAGAGTGGTTTTAAGACCGGGGTCTATGCACAAGGGTGGAGCTTGATTACTATCATCGAAGG
+GTGACTTGCCGTGTTACAATCGACAAGCGAACGGCCGACTGCTTCGGCCCGCTGAGCGGACAACCTCCGATGTACCTACT
+CCATAGTGGCTCGGGTCGATAATCACTATGCTCGTTAATCGTGCCATCCACTGCCCGCTTTAATCCCAACCGGCGTTTCT
+GCTACATGCTAGTCACGAAGGGGCGCCAGGGGATAGGCGAAAGCACTGGCTACGTCATCCTTGCAATAAAAACCGTTGCC
+TGGCACGGTCATCAAGTATCTCGCGTCGCCCAGTGGCCCC
diff --git a/test/data/simulate_input.sh b/test/data/simulate_input.sh
@@ -60,9 +60,9 @@ do
 done
 
 # Low error rate edge case
-error_rate=0.0009
+error_rate=0.001
 match_count=1
-match_length=1150
+match_length=1000
 echo "Generating $match_count reads of length $match_length with error rate $error_rate"
 generate_local_matches \
         --matches-out matches_e$error_rate.fasta \