Num observed != num assigned

COMBINE-lab · Nov 14, 2015 · 9a71b6c · 9a71b6c
1 parent 8456d6b
commit 9a71b6c
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/include/ReadExperiment.hpp b/include/ReadExperiment.hpp
@@ -162,6 +162,10 @@ class ReadExperiment {
 
     void setNumObservedFragments(uint64_t numObserved) { numObservedFragments_ = numObserved; }
 
+    uint64_t numObservedFragments() {
+        return numObservedFragments_;
+    }
+
     double mappingRate() {
         if (quantificationPasses_ > 0) {
             return static_cast<double>(numAssignedFragsInFirstPass_) / numObservedFragsInFirstPass_;

diff --git a/src/SalmonQuantify.cpp b/src/SalmonQuantify.cpp
@@ -3212,7 +3212,7 @@ transcript abundance from RNA-seq reads
         {
           bfs::path statPath = outputDirectory / "stats.tsv";
           std::ofstream statStream(statPath.string(), std::ofstream::out);
-          statStream << "numObservedFragments\t" << experiment.numMappedFragments() << '\n';
+          statStream << "numObservedFragments\t" << experiment.numObservedFragments() << '\n';
           for (auto& t : experiment.transcripts()) {
               auto l = (sopt.noEffectiveLengthCorrection) ? t.RefLength :
                   std::exp(t.getCachedLogEffectiveLength());