Changing logic of logo creation

Author: DanielOlson

src/SequenceWindow.cpp

@@ -102,12 +102,6 @@ void SequenceWindow::CalculateSymbolFrequencies() {
   }
 }
 
-/*
-bool SequenceWindow::operator<(const SequenceWindow& rhs) {
-    if (this->seqID != rhs.seqID)
-        return this->seqID < rhs.readID;
-    return (this->readID < rhs.readID);
-}*/
 
 SequenceWindow::SequenceWindow(unsigned long ml, unsigned long mo) {
 

src/repeat.cpp

@@ -54,7 +54,6 @@ void RepeatRegion::CreateLogo(SequenceWindow *window, UMatrix *matrix) {
            }*/
 
     }
-
     else if (fdesc.type == CT_DELETION) {
       deletions += fdesc.indelNumber;
       bplace += fdesc.indelNumber;
@@ -77,6 +76,9 @@ void RepeatRegion::CreateLogo(SequenceWindow *window, UMatrix *matrix) {
       i += bdesc.indelNumber;
     }
 
+    if (fplace > windowStart+repeatLength)
+      break;
+
     symbol s = window->seq[fplace];
     symbol sb = window->seq[bplace];
 

src/ultra.cpp

@@ -69,7 +69,6 @@ SequenceWindow *Ultra::GetSequenceWindow(SequenceWindow *seq, uthread *uth) {
     pthread_mutex_lock(&outerLock);
 
   // Check to see if we need to read more sequence first
-
   if (!reader->DoneReadingFile()) {
     if (!reader->IsReading()) {
       if (reader->ReadyWindowsSize() == 0) {