Merge branch 'develop' of github.com:COMBINE-lab/salmon into develop

include/AlevinOpts.hpp

@@ -50,6 +50,8 @@ struct AlevinOpts {
   bool just_align;
   //flag for deduplication
   bool noDedup;
+  //flag for not performing external whitelisting
+  bool noWhitelist;
   //Number of generator threads
   uint32_t numParsingThreads;
   //Number of consumer threads

include/BAMUtils.hpp

@@ -9,6 +9,7 @@ extern "C" {
 }
 
 #include <unordered_map>
+#include <string>
 
 namespace salmon {
   namespace bam_utils {

include/SalmonDefaults.hpp

@@ -128,6 +128,7 @@ namespace alevin {
 namespace defaults {
   constexpr const bool naiveEqclass{false};
   constexpr const bool noDedup{false};
+  constexpr const bool noWhitelist{false};
   constexpr const bool txpLevel{false};
   constexpr const bool eqClassLevel{false};
   constexpr const bool isDropseq{false};

src/AlevinUtils.cpp

@@ -571,6 +571,7 @@ namespace alevin {
       aopt.quiet = vm["quiet"].as<bool>();
       aopt.noEM = vm["noem"].as<bool>();
       aopt.noDedup = vm["noDedup"].as<bool>();
+      aopt.noWhitelist = vm["noWhitelist"].as<bool>();
       aopt.naiveEqclass = vm["naiveEqclass"].as<bool>();
       aopt.noQuant = vm["noQuant"].as<bool>();
       aopt.dumpfq = vm["dumpfq"].as<bool>();

src/CollapsedCellOptimizer.cpp

@@ -1355,7 +1355,7 @@ bool CollapsedCellOptimizer::optimize(EqMapT& fullEqMap,
   std::copy(geneNames.begin(), geneNames.end(), giterator);
   gFile.close();
 
-  if( not aopt.naiveEqclass and  not hasWhitelist and not usingHashMode){
+  if( not aopt.noWhitelist and  not aopt.naiveEqclass and  not hasWhitelist and not usingHashMode){
     aopt.jointLog->info("Clearing EqMap; Might take some time.");
     fullEqMap.clear();
 
@@ -1390,8 +1390,8 @@ bool CollapsedCellOptimizer::optimize(EqMapT& fullEqMap,
       aopt.jointLog->flush();
     }
   } //end-if whitelisting
-  else if ( usingHashMode and not hasWhitelist ) {
-    aopt.jointLog->warn("intelligent whitelisting is disabled in hash mode; skipping");
+  else if ( aopt.noWhitelist or ( usingHashMode and not hasWhitelist ) ) {
+    aopt.jointLog->warn("intelligent whitelisting is disabled ; skipping");
     aopt.jointLog->flush();
   }
 

src/ProgramOptionsGenerator.cpp

@@ -356,6 +356,9 @@ namespace salmon {
       (
        "naiveEqclass", po::bool_switch()->default_value(alevin::defaults::naiveEqclass),
        "Run naive per equivalence class deduplication, generating only total number of UMIs")
+      (
+       "noWhitelist", po::bool_switch()->default_value(alevin::defaults::noWhitelist),
+       "Stops the pipeline after UMI deduplication and quantification; not perform intelligent whitelisting.")
       (
        "noDedup", po::bool_switch()->default_value(alevin::defaults::noDedup),
        "Stops the pipeline after CB sequence correction and selective-alignment of reads.");