disabled deep copying for cuffnorm

matteodelucchi · May 6, 2014 · 566ebd3 · 566ebd3
1 parent 75617c9
commit 566ebd3
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Showing 5 changed files with 34 additions and 8 deletions.
diff --git a/cufflinks.xcodeproj/project.pbxproj b/cufflinks.xcodeproj/project.pbxproj
@@ -2047,7 +2047,7 @@
 				GCC_WARN_ABOUT_MISSING_FIELD_INITIALIZERS = NO;
 				GCC_WARN_ABOUT_MISSING_NEWLINE = NO;
 				GCC_WARN_EFFECTIVE_CPLUSPLUS_VIOLATIONS = NO;
-				GCC_WARN_NON_VIRTUAL_DESTRUCTOR = NO;
+				GCC_WARN_NON_VIRTUAL_DESTRUCTOR = YES;
 				GCC_WARN_SHADOW = NO;
 				GCC_WARN_UNINITIALIZED_AUTOS = NO;
 				GCC_WARN_UNUSED_FUNCTION = NO;
@@ -2092,6 +2092,7 @@
 				GCC_SYMBOLS_PRIVATE_EXTERN = NO;
 				GCC_UNROLL_LOOPS = YES;
 				GCC_VERSION = "";
+				GCC_WARN_NON_VIRTUAL_DESTRUCTOR = YES;
 				HEADER_SEARCH_PATHS = (
 					/opt/local/include,
 					/usr/include,
@@ -2744,6 +2745,7 @@
 				GCC_SYMBOLS_PRIVATE_EXTERN = NO;
 				GCC_VERSION = "";
 				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
+				GCC_WARN_NON_VIRTUAL_DESTRUCTOR = YES;
 				GCC_WARN_UNINITIALIZED_AUTOS = NO;
 				HEADER_SEARCH_PATHS = (
 					/opt/local/include,
@@ -2783,6 +2785,7 @@
 				GCC_UNROLL_LOOPS = YES;
 				GCC_VERSION = "";
 				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
+				GCC_WARN_NON_VIRTUAL_DESTRUCTOR = YES;
 				GCC_WARN_UNINITIALIZED_AUTOS = YES;
 				GENERATE_PROFILING_CODE = YES;
 				HEADER_SEARCH_PATHS = (

diff --git a/src/bundles.h b/src/bundles.h
@@ -217,6 +217,7 @@ class BundleFactory
 		_rg_props = boost::shared_ptr<ReadGroupProperties>(new ReadGroupProperties(fac->read_group_properties()));
 	}
 
+    virtual ~BundleFactory() {} 
     boost::shared_ptr<const HitFactory> hit_factory() const { return _hit_fac; }
 
     bool bundles_remain()  
@@ -260,16 +261,24 @@ class BundleFactory
 	}
 
     // This function NEEDS to deep copy the ref_mRNAs, otherwise cuffdiff'd
-    // samples will clobber each other
-    void set_ref_rnas(const vector<boost::shared_ptr<Scaffold> >& mRNAs)
+    // samples will clobber each other. Deep copying is necessary whenever
+    // you need to set fpkm or num fragments in Scaffold objects (e.g. during bias correction or multiread correction)
+    void set_ref_rnas(const vector<boost::shared_ptr<Scaffold> >& mRNAs, bool deep_copy = true)
     {
 #if ENABLE_THREADS
         boost::mutex::scoped_lock lock(_factory_lock);
 #endif
         ref_mRNAs.clear();
-        for (vector<boost::shared_ptr<Scaffold> >::const_iterator i = mRNAs.begin(); i < mRNAs.end(); ++i)
+        if (deep_copy)
         {
-            ref_mRNAs.push_back(boost::shared_ptr<Scaffold>(new Scaffold(**i)));
+            for (vector<boost::shared_ptr<Scaffold> >::const_iterator i = mRNAs.begin(); i < mRNAs.end(); ++i)
+            {
+                ref_mRNAs.push_back(boost::shared_ptr<Scaffold>(new Scaffold(**i)));
+            }
+        }
+        else
+        {
+            ref_mRNAs = mRNAs;
         }
 
         RefID last_id = 0;

diff --git a/src/cuffnorm.cpp b/src/cuffnorm.cpp
@@ -644,7 +644,10 @@ void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* norm_stand
 
     BOOST_FOREACH (boost::shared_ptr<ReplicatedBundleFactory> fac, bundle_factories)
     {
-        fac->set_ref_rnas(ref_mRNAs);
+        // NOTE: we aren't deep copying here to save memory.  We can pull this off
+        // because unless bias correction or multiread correction is enabled,
+        // we don't need to write into Scaffold objects.
+        fac->set_ref_rnas(ref_mRNAs, false);
         if (mask_gtf) 
             fac->set_mask_rnas(mask_rnas);
     }

diff --git a/src/differential.h b/src/differential.h
@@ -163,6 +163,8 @@ struct TestLauncher
     {
     }
 
+    virtual ~TestLauncher() {} 
+
     void operator()();
 
     void register_locus(const string& locus_id);
@@ -239,6 +241,7 @@ class TrackingDataWriter : public TestLauncher
             }
         }
         fprintf(fout, "\n");
+        fflush(fout);
     }
 
     void print_count_tracking_header(FILE* fout,
@@ -256,6 +259,7 @@ class TrackingDataWriter : public TestLauncher
             }
         }
         fprintf(fout, "\n");
+        fflush(fout);
     }
 
     void print_FPKM_simple_table_header(FILE* fout,
@@ -277,6 +281,7 @@ class TrackingDataWriter : public TestLauncher
                     fprintf(fout, "\t%s_%d", condition_name.c_str(), rep_num);
                 }
             }
+            fflush(fout);
         }
     }
 
@@ -299,6 +304,7 @@ class TrackingDataWriter : public TestLauncher
                     fprintf(fout, "\t%s_%d", condition_name.c_str(), rep_num);
                 }
             }
+            fflush(fout);
         }
     }
 
@@ -380,6 +386,7 @@ class TrackingDataWriter : public TestLauncher
             }
 
             fprintf(fout, "\n");
+            fflush(fout);
         }
     }
 
@@ -437,6 +444,7 @@ class TrackingDataWriter : public TestLauncher
             }
 
             fprintf(fout, "\n");
+            fflush(fout);
         }
     }
 
@@ -462,6 +470,7 @@ class TrackingDataWriter : public TestLauncher
                     fprintf(fout, "\t%lg", FPKM);
                 }
             }
+            fflush(fout);
         }
     }
 
@@ -487,6 +496,7 @@ class TrackingDataWriter : public TestLauncher
                     fprintf(fout, "\t%lg", count);
                 }
             }
+            fflush(fout);
         }
     }
 
@@ -567,6 +577,7 @@ class TrackingDataWriter : public TestLauncher
                             status_str);
                 }
             }
+            fflush(fout);
         }
     }
 

diff --git a/src/replicates.h b/src/replicates.h
@@ -441,14 +441,14 @@ class ReplicatedBundleFactory
 
     // This function NEEDS to deep copy the ref_mRNAs, otherwise cuffdiff'd
     // samples will clobber each other
-    void set_ref_rnas(const vector<boost::shared_ptr<Scaffold> >& mRNAs)
+    void set_ref_rnas(const vector<boost::shared_ptr<Scaffold> >& mRNAs, bool deep_copy = true)
     {
 #if ENABLE_THREADS
         boost::mutex::scoped_lock lock(_rep_factory_lock);
 #endif
         BOOST_FOREACH(boost::shared_ptr<BundleFactory> fac, _factories)
         {
-            fac->set_ref_rnas(mRNAs);
+            fac->set_ref_rnas(mRNAs, deep_copy);
         }
     }