Merge branch 'preprint-testing'

COMBINE-lab · Jun 26, 2015 · 21bf89a · 21bf89a
2 parents f9d56f8 + 57aec9a
commit 21bf89a
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Showing 6 changed files with 283 additions and 84 deletions.
diff --git a/include/EquivalenceClassBuilder.hpp b/include/EquivalenceClassBuilder.hpp
@@ -63,13 +63,17 @@ class EquivalenceClassBuilder {
 
         bool finish() {
             active_ = false;
+            size_t totalCount{0};
             for (auto kv = countMap_.begin(); !kv.is_end(); ++kv) {
                 kv->second.normalizeAux();
+                totalCount += kv->second.count;
                 countVec_.push_back(*kv);
             }
 
     	    logger_->info("Computed {} rich equivalence classes "
 			  "for further processing", countVec_.size());
+            logger_->info("Counted {} total reads in the equivalence classes ",
+                    totalCount);
             return true;
         }
 

diff --git a/include/SalmonOpts.hpp b/include/SalmonOpts.hpp
@@ -26,10 +26,13 @@ struct SalmonOpts {
     bool maxMEMIntervals; // If true, don't split (S)MEMs into MEMs
     */
 
-    SalmonOpts() : splitSpanningSeeds(false), noFragLengthDist(false),
+    SalmonOpts() : allowOrphans(false), splitSpanningSeeds(false), noFragLengthDist(false),
                    noEffectiveLengthCorrection(false), useReadCompat(false),
                    maxReadOccs(200), extraSeedPass(false),
                    mappingCacheMemoryLimit(5000000) {}
+
+    bool allowOrphans; // Consider orphaned reads when performing lightweight alignemnt.
+
     bool splitSpanningSeeds; // Attempt to split seeds that span multiple transcripts.
 
     bool noFragLengthDist; // Do not give a fragment assignment a likelihood based on an emperically

diff --git a/include/Transcript.hpp b/include/Transcript.hpp
@@ -109,8 +109,12 @@ class Transcript {
         return std::numeric_limits<uint8_t>::max();
     }
 
+    inline void setSharedCount(double sc) {
+        sharedCount_.store(sc);
+    }
+
     inline void addSharedCount(double sc) {
-	salmon::utils::incLoop(sharedCount_, sc);
+	    salmon::utils::incLoop(sharedCount_, sc);
     }
 
     inline void setLastTimestepUpdated(uint64_t currentTimestep) {

diff --git a/src/CollapsedEMOptimizer.cpp b/src/CollapsedEMOptimizer.cpp
@@ -274,7 +274,10 @@ size_t markDegenerateClasses(
             errstream << "}\n";
             errstream << "============================\n\n";
 
-            jointLog->info(errstream.str());
+            bool verbose{false};
+            if (verbose) {
+                jointLog->info(errstream.str());
+            }
             ++numDropped;
             kv.first.setValid(false);
         }
@@ -405,7 +408,6 @@ bool CollapsedEMOptimizer::optimize(ExpT& readExp,
       alphaSum += alphas[i];
     }
 
-
     if (alphaSum < minWeight) {
         jointLog->error("Total alpha weight was too small! "
                         "Make sure you ran salmon correclty.");
@@ -417,9 +419,9 @@ bool CollapsedEMOptimizer::optimize(ExpT& readExp,
     for (size_t i = 0; i < transcripts.size(); ++i) {
         // Set the mass to the normalized (after truncation)
         // relative abundance
+        transcripts[i].setSharedCount(alphas[i]);
         transcripts[i].setMass(alphas[i] / alphaSum);
     }
-
     return true;
 }