adding back test, fixing issue with trailing tab

andersen-lab · Apr 11, 2022 · 2b455d7 · 2b455d7
1 parent ba09b79
commit 2b455d7
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 8 deletions.
diff --git a/src/ref_seq.cpp b/src/ref_seq.cpp
@@ -137,7 +137,7 @@ int ref_antd::codon_aa_stream(std::string region, std::ostringstream &line_strea
     //adding amino acid position
     int64_t start = it->get_start();
     int64_t aa_pos = ((pos - start) / 3)+1;
-    fout << aa_pos << "\t";
+    fout << aa_pos;
     fout << std::endl;
 
     delete[] ref_codon;

diff --git a/tests/test_variants.cpp b/tests/test_variants.cpp
@@ -27,23 +27,22 @@ int call_var_check_outfile(std::string prefix, uint8_t min_qual, uint8_t min_dep
 int main() {
   int num_success = 0;
   // Quality threshold 20. Frequency threshold: 0.03. Total_DP = 3. Indel passes filters with total_depth 4. Has two lines.
-  std::string t_20_02_1[3] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneKatyPerry:id-test3\tAAG\tK\tATG\tM\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneTaylorSwift:id-testedit2\tAGA\tR\tTGA\t*\t70"};
-  //"test\t210\tA\t+GT\t1\t1\t41\t1\t0\t20\t0.25\t4\t0.4\tFALSE\tNA\tNA\tNA\tNA\tNA\tNA"};
+  std::string t_20_02_1[4] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneKatyPerry:id-test3\tAAG\tK\tATG\tM\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneTaylorSwift:id-testedit2\tAGA\tR\tTGA\t*\t70", "test\t210\tA\t+GT\t1\t1\t41\t1\t0\t20\t0.25\t4\t0.4\tFALSE\tNA\tNA\tNA\tNA\tNA\tNA"};
   // Quality threshold 3-. Frequency threshold: 0.03. Total_DP = 3. Freq = 0.666667 No Indel
   std::string t_20_03[3] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneKatyPerry:id-test3\tAAG\tK\tATG\tM\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD\t70", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tgeneTaylorSwift:id-testedit2\tAGA\tR\tTGA\t*\t70"};
   // Quality threshold 25. Frequency threshold: 0.03. Total_DP = 2. Freq = 0.5 No Indel.
   std::string t_25_03[3] = {"test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tgeneKatyPerry:id-test3\tAAG\tK\tATG\tM\t70", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD\t70", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tgeneTaylorSwift:id-testedit2\tAGA\tR\tTGA\t*\t70"};
   // Minimum depth threshold. Should be empty
   std::string t_25_03_20[] = {};
-  num_success = call_var_check_outfile("../data/test.indel", 20, 0, 0.02, t_20_02_1, 3);
+  num_success = call_var_check_outfile("../data/test.indel", 20, 0, 0.02, t_20_02_1, 4);
   std::cout << num_success << std::endl;
-  num_success += call_var_check_outfile("../data/test.indel", 20, 0, 0.03, t_20_03, 3);
+  num_success += call_var_check_outfile("../data/test.indel2", 20, 0, 0.03, t_20_03, 3);
   std::cout << num_success << std::endl;
-  num_success += call_var_check_outfile("../data/test.indel", 25, 0, 0.03, t_25_03, 3);
+  num_success += call_var_check_outfile("../data/test.indel3", 25, 0, 0.03, t_25_03, 3);
   std::cout << num_success << std::endl;
-  num_success += call_var_check_outfile("../data/test.indel", 25, 20, 0.03, t_25_03_20, 0);
+  num_success += call_var_check_outfile("../data/test.indel4", 25, 20, 0.03, t_25_03_20, 0);
   std::cout << num_success << std::endl;
-  if(num_success == 9)
+  if(num_success == 0)
     return 0;
   return -1;
 }