1.0.4 (#77)

* trying to change class initializaiton to fix the bug reported in #76

* Changing auto* to auto to stop issue 76

* Changing auto* to auto to stop issue 76

* Updating the format of estimated false discovery rate output

* Fixed a bug with calculating coverage

Author: DanielOlson

src/FASTAReader.hpp

@@ -25,8 +25,8 @@ class FASTAReader {
   std::ifstream file;
 
   std::string line;
-  long long linePlace;
-  unsigned long long total_seq_length;
+  long long linePlace = 0;
+  unsigned long long total_seq_length = 0;
 
   // change to queues
   std::vector<SequenceWindow *> windows;
@@ -46,12 +46,12 @@ class FASTAReader {
   double G_pctg;
 
   symbol *overlapBuffer;          //    = NULL;
-  unsigned long overlapLength;    //    = 0;
+  unsigned long overlapLength = 0;    //    = 0;
 
-  std::string sequenceName;       // = "";
-  unsigned long sequenceID;       // = 0;
-  unsigned long readID;           // = 0; // read id's may not be contiguous
-  unsigned long symbolsReadInSeq; // = 0;
+  std::string sequenceName = "";       // = "";
+  unsigned long sequenceID = 0;       // = 0;
+  unsigned long readID = 0;           // = 0; // read id's may not be contiguous
+  unsigned long symbolsReadInSeq = 0; // = 0;
 
   bool doneReadingFile;           //  = false;
   bool isReading;

src/cli.hpp

@@ -5,7 +5,7 @@
 #ifndef ULTRA_CLI_HPP
 #define ULTRA_CLI_HPP
 
-#define ULTRA_VERSION_STRING "1.0.3"
+#define ULTRA_VERSION_STRING "1.0.4"
 #define DEBUG_STRING ""
 #ifdef DEBUG_PRAGMA
 #undef DEBUG_STRING

src/main.cpp

@@ -71,7 +71,7 @@ int main_wrapper(int argc, const char * argv[]) {
       search_setting.bed_out = false;
 
       // We first get the normal coverage
-      auto *ultra = new Ultra(&search_setting);
+      auto ultra = new Ultra(&search_setting);
       ultra->AnalyzeFile();
       ultra->OutputRepeats(true);
       seq_length = ultra->reader->fastaReader->total_seq_length;
@@ -102,7 +102,7 @@ int main_wrapper(int argc, const char * argv[]) {
         }
       }
 
-      printf("(%zu/%zu): %g, %g, %s\n",(coverage.size()),
+      printf("(%zu/%zu): %.5f, %.5f, %s\n",(coverage.size()),
              param_strings.size(),
              real_coverage, fdr, arg_string.c_str());
     }
@@ -113,7 +113,7 @@ int main_wrapper(int argc, const char * argv[]) {
       double false_coverage = (double)shuffled_coverage[best_coverage_index] / (double)seq_length;
       double fdr = false_coverage / real_coverage;
 
-      printf("Best coverage within FDR limit: %g, %g, %s\n", real_coverage,
+      printf("Best coverage within FDR limit: %.5f, %.5f, %s\n", real_coverage,
              fdr,
              param_strings[best_coverage_index].c_str());
 
@@ -136,9 +136,7 @@ int main_wrapper(int argc, const char * argv[]) {
   }
 
   // Perform the actual run
-
-
-  auto *ultra = new Ultra(settings);
+  auto ultra = new Ultra(settings);
   ultra->AnalyzeFile();
   ultra->OutputRepeats(true);
   unsigned long long true_coverage = ultra->Coverage();

src/ultra.cpp

@@ -322,6 +322,10 @@ void Ultra::OutputRepeat(RepeatRegion *r, bool isSubRep) {
     total_coverage += (r->sequenceStart + r->repeatLength) - rep_start;
   }
 
+  if (r->sequenceStart + r->repeatLength > last_rep_end) {
+    last_rep_end = r->sequenceStart + r->repeatLength;
+  }
+
   if (!settings->suppress_out)
     for (auto writer : writers)
       writer->WriteRepeat(r);

src/ultra.hpp

@@ -68,7 +68,7 @@ class Ultra {
   bool firstRepeat = true;
   unsigned long repeatBuffer = 2000;
 
-  unsigned long long total_coverage;
+  unsigned long long total_coverage = 0;
   int last_read_id = 0;
   unsigned long long last_rep_end = 0;