Author: Michael R. Crusoe <crusoe@ucdavis.edu>
Description: fix upstream's typos
--- salmon.orig/CMakeLists.txt
+++ salmon/CMakeLists.txt
@@ -6,12 +6,12 @@
 
 set(CPACK_PACKAGE_VERSION "0.4.2")
 set(CPACK_PACKAGE_VERSION_MAJOR "0")
-set(CPACK_PACKAGE_VERSION_MINOR 4")
-set(CPACK_PACKAGE_VERSION_PATCH 2")
+set(CPACK_PACKAGE_VERSION_MINOR "4")
+set(CPACK_PACKAGE_VERSION_PATCH "2")
 set(CPACK_GENERATOR "TGZ")
 set(CPACK_SOURCE_GENERATOR "TGZ")
-set(CPACK_PACKAGE_VENDOR Stony Brook University")
-set(CPACK_PACKAGE_DESCRIPTION_SUMMARY Salmon - Wicked-fast RNA-seq isoform quantification using lightweight alignments")
+set(CPACK_PACKAGE_VENDOR "Stony Brook University")
+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Salmon - Wicked-fast RNA-seq isoform quantification using lightweight alignments")
 set(CPACK_PACKAGE_NAME 
   "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
 set(CPACK_SOURCE_PACKAGE_FILE_NAME
--- salmon.orig/include/tensemble/GBMRegressor.h
+++ salmon/include/tensemble/GBMRegressor.h
@@ -63,7 +63,7 @@
     if (loss_function==SQUARE_LOSS) {
         loss=new SquareLoss();
     }else {
-        fprintf(stderr, "Error: Unknow loss function\n");
+        fprintf(stderr, "Error: Unknown loss function\n");
         return ENSEMBLE_FAIL;
     }
     //allocate memory for prior and trees
--- salmon.orig/include/tensemble/cmdline.h
+++ salmon/include/tensemble/cmdline.h
@@ -91,7 +91,7 @@
                 value[s] = "";
             }
         } else {
-            fprintf(stderr, "Error: Unknow parameter %s.\n",s.c_str());
+            fprintf(stderr, "Error: Unknown parameter %s.\n",s.c_str());
             print_help();
             return false;
         }
@@ -135,7 +135,7 @@
             }
         }
         if (i==len) {
-            fprintf(stderr, "Error: Unknow parameter %s.\n",iter->first.c_str());
+            fprintf(stderr, "Error: Unknown parameter %s.\n",iter->first.c_str());
 //            print_help();
             return false;
         }
--- salmon.orig/src/SalmonQuantify.cpp
+++ salmon/src/SalmonQuantify.cpp
@@ -2928,7 +2928,7 @@
                                         "many reads, then just keep the data in memory for subsequent rounds of inference. Obviously, this value should "
                                         "not be too large if you wish to keep a low memory usage, but setting it large enough can substantially speed up "
                                         "inference on \"small\" files that contain only a few million reads.")
-    ("maxOcc,m", po::value<int>(&(memOptions->max_occ))->default_value(200), "(S)MEMs occuring more than this many times won't be considered.")
+    ("maxOcc,m", po::value<int>(&(memOptions->max_occ))->default_value(200), "(S)MEMs occurring more than this many times won't be considered.")
     ("maxReadOcc,w", po::value<uint32_t>(&(sopt.maxReadOccs))->default_value(100), "Reads \"mapping\" to more than this many places won't be considered.")
     ("noEffectiveLengthCorrection", po::bool_switch(&(sopt.noEffectiveLengthCorrection))->default_value(false), "Disables "
                         "effective length correction when computing the probability that a fragment was generated "
