Oct 15, 2024: Freeze

vgl-hub · Oct 15, 2024 · 7066c14 · 7066c14
1 parent cfb1e5b
commit 7066c14
Showing 1 changed file with 3 additions and 10 deletions.
diff --git a/src/teloscope.cpp b/src/teloscope.cpp
@@ -281,9 +281,9 @@ SegmentData Teloscope::analyzeSegment(std::string &sequence, UserInputTeloscope
         WindowData windowData = prevOverlapData;
         analyzeWindow(window, windowStart, windowData, nextOverlapData);
 
-        if (userInput.modeGC) {windowData.gcContent = getGCContent(windowData.nucleotideCounts, window.size());}
-        if (userInput.modeEntropy) {windowData.shannonEntropy = getShannonEntropy(windowData.nucleotideCounts, window.size());}
-        if (userInput.modeMatch) {getPatternDensities(windowData, window.size());}
+        if (userInput.modeGC) { windowData.gcContent = getGCContent(windowData.nucleotideCounts, window.size()); }
+        if (userInput.modeEntropy) { windowData.shannonEntropy = getShannonEntropy(windowData.nucleotideCounts, window.size()); }
+        if (userInput.modeMatch) { getPatternDensities(windowData, window.size()); }
 
         // Update windowData
         windowData.windowStart = windowStart + absPos;
@@ -298,9 +298,6 @@ SegmentData Teloscope::analyzeSegment(std::string &sequence, UserInputTeloscope
         };
 
         for (const auto& [groupName, matches] : patternMatches) {
-            if (windowData.canonicalCounts >= 2 || windowData.nonCanonicalCounts >= 4) { // JACK: Add to user cutoffs
-                auto winBlocks = getTelomereBlocks(matches, windowData.windowStart);
-                segmentBlocks[groupName].insert(segmentBlocks[groupName].end(), winBlocks.begin(), winBlocks.end());
             if (windowData.canonicalCounts >= 2 || windowData.nonCanonicalCounts >= 4) { // JACK: Add to user cutoffs
                 auto winBlocks = getTelomereBlocks(matches, windowData.windowStart);
                 segmentBlocks[groupName].insert(segmentBlocks[groupName].end(), winBlocks.begin(), winBlocks.end());
@@ -310,11 +307,9 @@ SegmentData Teloscope::analyzeSegment(std::string &sequence, UserInputTeloscope
         // Pass and reset overlap data
         prevOverlapData = nextOverlapData;
         nextOverlapData = WindowData(); // Reset for next iteration
-        nextOverlapData = WindowData(); // Reset for next iteration
 
         // Prepare next window
         windowStart += step;
-        if (windowStart >= sequenceSize) {
         if (windowStart >= sequenceSize) {
             break;
         }
@@ -443,12 +438,10 @@ void Teloscope::handleBEDFile() {
         shannonFile.open(userInput.outRoute + "/shannonEntropy.bedgraph");
     }
 
-    if (userInput.keepWindowData && userInput.modeGC) {
     if (userInput.keepWindowData && userInput.modeGC) {
         gcContentFile.open(userInput.outRoute + "/gcContent.bedgraph");
     }
 
-    if (userInput.keepWindowData && userInput.modeMatch) {
     if (userInput.keepWindowData && userInput.modeMatch) {
 
         for (const auto& pattern : userInput.patterns) {