From: Michael R. Crusoe <crusoe@debian.org>
Subject: fix typos
Forwarded: https://github.com/COMBINE-lab/salmon/pull/548/
--- salmon.orig/include/BAMQueue.tpp
+++ salmon/include/BAMQueue.tpp
@@ -153,7 +153,7 @@
     AlignmentGroup<FragT*>* grp;
     //while(!alnGroupPool_.empty()) { alnGroupPool_.pop(grp); delete grp; grp = nullptr; }
     while(alnGroupPool_.try_dequeue(grp)) { delete grp; grp = nullptr; }
-    fmt::print(stderr, "\nEmptied Alignemnt Group Pool. . ");
+    fmt::print(stderr, "\nEmptied Alignment Group Pool. . ");
     while(alnGroupQueue_.try_dequeue(grp)) { delete grp; grp = nullptr; }
     fmt::print(stderr, "\nEmptied Alignment Group Queue. . . ");
     fmt::print(stderr, "done\n");
@@ -337,7 +337,7 @@
     if (!mateIsMapped and !readIsMapped) {
         return AlignmentType::UnmappedPair;
     }
-    std::cerr << "\n\n\nEncountered unknown alignemnt type; this should not happen!\n"
+    std::cerr << "\n\n\nEncountered unknown alignment type; this should not happen!\n"
               << "Please file a bug report on GitHub. Exiting.\n";
     std::exit(1);
 }
@@ -410,7 +410,7 @@
                     break;
                     // === end if MappedDiscordantPair case
                 default:
-                    logger_->error("\n\n\nEncountered unknown alignemnt type; this should not happen!\n"
+                    logger_->error("\n\n\nEncountered unknown alignment type; this should not happen!\n"
                                    "Please file a bug report on GitHub. Exiting.\n");
                     std::exit(1);
                     break;
@@ -531,7 +531,7 @@
                 }
                 break;
             default:
-                logger_->error("\n\n\nEncountered unknown alignemnt type; this should not happen!\n"
+                logger_->error("\n\n\nEncountered unknown alignment type; this should not happen!\n"
                                "Please file a bug report on GitHub. Exiting.\n");
                 std::exit(1);
                 break;
--- salmon.orig/include/SalmonOpts.hpp
+++ salmon/include/SalmonOpts.hpp
@@ -48,7 +48,7 @@
                             // the optimization.
 
   bool allowOrphans; // Consider orphaned reads when performing lightweight
-                     // alignemnt.
+                     // alignment.
 
   std::string auxDir; // The directory where auxiliary files will be written.
 
--- salmon.orig/src/ProgramOptionsGenerator.cpp
+++ salmon/src/ProgramOptionsGenerator.cpp
@@ -232,7 +232,7 @@
        "[selective-alignment mode only] : Allow soft-clipping of reads that overhang the beginning or ends "
        "of the transcript.  In this case, the overhaning section of the read will simply be unaligned, and "
        "will not contribute or detract from the alignment score.  The default policy is to force an end-to-end "
-       "alignemnt of the entire read, so that overhanings will result in some deletion of nucleotides from the "
+       "alignment of the entire read, so that overhanings will result in some deletion of nucleotides from the "
        "read."
        )
       ("fullLengthAlignment", 
@@ -575,7 +575,7 @@
        po::bool_switch(&(sopt.alternativeInitMode))->default_value(salmon::defaults::alternativeInitMode),
        "[Experimental]: Use an alternative strategy (rather than simple "
        "interpolation between) the "
-       "online and uniform abundance estimates to initalize the EM / VBEM "
+       "online and uniform abundance estimates to initialize the EM / VBEM "
        "algorithm.")
       ("auxDir",
        po::value<std::string>(&(sopt.auxDir))->default_value(salmon::defaults::auxDir),
@@ -710,7 +710,7 @@
        "purpose "
        "of ignoring the auxiliary models for the first "
        "<numPreAuxModelSamples> observations is to avoid applying these "
-       "models before thier "
+       "models before their "
        "parameters have been learned sufficiently well.")
       ("useEM", po::bool_switch(&(sopt.useEM))->default_value(salmon::defaults::useEM),
        "Use the traditional EM algorithm for optimization in the batch passes.")
--- salmon.orig/src/Salmon.cpp
+++ salmon/src/Salmon.cpp
@@ -256,7 +256,7 @@
       return help(opts);
     } else {
       // If the command is quant; determine whether
-      // we're quantifying with raw sequences or alignemnts
+      // we're quantifying with raw sequences or alignments
       if (cmdMain->first == "quant") {
 
         if (subCommandArgc < 2) {
--- salmon.orig/src/AlevinUtils.cpp
+++ salmon/src/AlevinUtils.cpp
@@ -723,7 +723,7 @@
             allNflag = false;
           }
           if (found==std::string::npos){
-            aopt.jointLog->error("\nERROR: Wrong IUPAC charachter {} in {}\n"
+            aopt.jointLog->error("\nERROR: Wrong IUPAC character {} in {}\n"
                                  "\nExiting now: Please check "
                                  "https://www.bioinformatics.org/sms/iupac.html"
                                  "for more details about iupac.",
--- salmon.orig/include/spdlog/details/async_log_helper.h
+++ salmon/include/spdlog/details/async_log_helper.h
@@ -282,7 +282,7 @@
         }
         catch(...)
         {
-            _err_handler("Unknown exeption in async logger worker loop.");
+            _err_handler("Unknown exception in async logger worker loop.");
         }
     }
     if (_worker_teardown_cb) _worker_teardown_cb();
--- salmon.orig/src/CollapsedCellOptimizer.cpp
+++ salmon/src/CollapsedCellOptimizer.cpp
@@ -521,7 +521,7 @@
 
     if (alphaSum < minWeight) {
       jointlog->error("Total alpha weight was too small! "
-                      "Make sure you ran salmon correclty.");
+                      "Make sure you ran salmon correctly.");
       jointlog->flush();
       return false;
     }
--- salmon.orig/src/CollapsedEMOptimizer.cpp
+++ salmon/src/CollapsedEMOptimizer.cpp
@@ -510,7 +510,7 @@
 
     if (alphaSum < ::minWeight) {
       jointLog->error("Total alpha weight was too small! "
-                      "Make sure you ran salmon correclty.");
+                      "Make sure you ran salmon correctly.");
       return false;
     }
 
@@ -803,7 +803,7 @@
       alphas[i].store(alphasPrime[i].load());
       alphasPrime[i] = 1.0;
     }
-  } else { // otherwise, initalize with a linear combination of the true and
+  } else { // otherwise, initialize with a linear combination of the true and
            // uniform alphas
     for (size_t i = 0; i < alphas.size(); ++i) {
       auto uniAbund = (metaGenomeMode or altInitMode) ? alphasPrime[i].load()
@@ -980,7 +980,7 @@
   /* -- v0.8.x
   if (alphaSum < ::minWeight) {
     jointLog->error("Total alpha weight was too small! "
-                    "Make sure you ran salmon correclty.");
+                    "Make sure you ran salmon correctly.");
     return false;
   }
   */
@@ -1005,7 +1005,7 @@
 
   if (alphaSum < ::minWeight) {
     jointLog->error("Total alpha weight was too small! "
-                    "Make sure you ran salmon correclty.");
+                    "Make sure you ran salmon correctly.");
     return false;
   }
 
