Fix lib_format_counts.json

Don't write any entries for format encodings that
don't correspond to a valid library type (e.g.
single end with SF, SR, etc.).  There are only 12
possible valid library types, and there should
be only 12 entires corresponding to counts:

U
SF
SR
IU
OU
MU
ISR
OSR
MSR
ISF
OSF
MSF

This commit fixes #82.

Note: We should write out lib_format_counts.json in
alignment-based mode.

include/LibraryFormat.hpp

@@ -89,11 +89,17 @@ class LibraryFormat {
         if (type == ReadType::SINGLE_END) {
             if (orientation != ReadOrientation::NONE) {
                 return desc;
+            } else if (strandedness == ReadStrandedness::SA or 
+                       strandedness == ReadStrandedness::AS ) {
+                return desc;
             }
         }
         if (type == ReadType::PAIRED_END) {
             if (orientation == ReadOrientation::NONE) {
                 return desc;
+            } else if (strandedness == ReadStrandedness::S or 
+                       strandedness == ReadStrandedness::A ) {
+                return desc;
             }
         }
 
@@ -131,26 +137,15 @@ class LibraryFormat {
             desc += "SR";
             break;
         case ReadStrandedness::S:
-            desc += "F";
+            desc += "SF";
             break;
         case ReadStrandedness::A:
-            desc += "R";
+            desc += "SR";
             break;
         case ReadStrandedness::U:
             desc += "U";
             break;
         }
-        /*
-        if (type == ReadType::PAIRED_END) {
-            if (desc == "SF" or 
-                desc == "SR" or
-                desc == "F" or
-                desc == "R" or 
-                desc == "U" ) { 
-                desc.clear();
-            }
-        }
-        */
         return desc;
     }
 

include/ReadExperiment.hpp

@@ -600,13 +600,20 @@ class ReadExperiment {
             }
 
             //ofile << "---- counts for each format type ---\n";
+            //std::unordered_map<std::string, uint64_t> descMap;
             for (size_t i = 0; i < counts.size(); ++i) {
                 //ofile << LibraryFormat::formatFromID(i) << " : " << counts[i] << "\n";
                 std::string desc = LibraryFormat::formatFromID(i).toString();
                 if (!desc.empty()) {
                     oa(cereal::make_nvp(desc, counts[i].load()));
+                    //descMap[desc] += counts[i].load();
                 }
             }
+            /*
+            for (auto& kv : descMap) {
+                oa(cereal::make_nvp(kv.first, kv.second));
+            }
+            */
             //ofile << "------------------------------------\n\n";
         }
         //ofile.close();