integrate cigar generation

Author: Hossein Asghari

include/Util.hpp

@@ -397,13 +397,11 @@ Compile-time selection between list-like and map-like printing.
         std::vector<int32_t> cigar_counts;
         std::string cigar_types;
         int32_t begin_softclip_len{0}, end_softclip_len{0};
-        bool beginOverhang{false}, endOverhang{false};
         // bool allowOverhangSoftClip{false};
 
         void clear() {
           cigar_counts.clear(); cigar_types.clear();
           begin_softclip_len = end_softclip_len = 0;
-          beginOverhang = endOverhang = false;
         }
 
         void add_item(int32_t count, char type) {
@@ -414,13 +412,13 @@ Compile-time selection between list-like and map-like printing.
         // void get_approx_cigar(int32_t readLen, std::string& cigar) {
         //   if (begin_softclip_len > 0) {
         //     cigar += std::to_string(begin_softclip_len);
-        //     cigar += beginOverhang and allowOverhangSoftClip ? "I" : "S";
+        //     cigar += allowOverhangSoftClip ? "I" : "S";
         //   }
         //   cigar += std::to_string(readLen - (begin_softclip_len + end_softclip_len));
         //   cigar += "M";
         //   if (end_softclip_len > 0) {
         //     cigar += std::to_string(end_softclip_len);
-        //     cigar += endOverhang and allowOverhangSoftClip ? "I" : "S";
+        //     cigar += allowOverhangSoftClip ? "I" : "S";
         //   }
         // }
 
@@ -485,11 +483,6 @@ Compile-time selection between list-like and map-like printing.
           if (cigar_counts.size() != cigar_types.size()) return "!";
 
           std::string cigar = "";
-          if (begin_softclip_len > 0) {
-            cigar += std::to_string(begin_softclip_len);
-            cigar += 'S';
-          }
-          // 
           int32_t last_count = cigar_counts[0];
           char last_type = cigar_types[0];
           for (size_t i = 1; i < cigar_counts.size(); i++) {
@@ -507,11 +500,6 @@ Compile-time selection between list-like and map-like printing.
           // add last
           cigar += std::to_string(last_count);
           cigar += last_type;
-          // 
-          if (end_softclip_len > 0) {
-            cigar += std::to_string(end_softclip_len);
-            cigar += 'S';
-          }
           return cigar;
         }
       };

src/PuffAligner.cpp

@@ -591,7 +591,8 @@ bool PuffAligner::alignRead(std::string& read, std::string& read_rc, const std::
           {
             part_score = ez.max;
             openGapLen = ez.max_t + 1;
-            cigarGen.begin_softclip_len = readWindow.length() - (ez.max_q + 1);
+            cigarGen.add_item(readWindow.length() - (ez.max_q + 1), 'S');
+
           }
           alignmentScore += part_score;
           addCigar(cigarGen, ez, true);
@@ -613,8 +614,7 @@ bool PuffAligner::alignRead(std::string& read, std::string& read_rc, const std::
 
           if (mopts.computeCIGAR) {
             if (allowSoftclip && remainedSoftClipLen >= 0) {
-              cigarGen.begin_softclip_len = firstMemStart_read;
-              cigarGen.beginOverhang = true;
+              cigarGen.add_item(firstMemStart_read, 'S');
               openGapLen = 0;
             } else {
               cigarGen.add_item(firstMemStart_read, 'I');
@@ -860,7 +860,7 @@ bool PuffAligner::alignRead(std::string& read, std::string& read_rc, const std::
           else
           {
             part_score = ez.max;
-            cigarGen.end_softclip_len = readWindow.length() - (ez.max_q + 1);
+            cigarGen.add_item(readWindow.length() - (ez.max_q + 1), 'S');
           }
           alignmentScore += part_score;
           addCigar(cigarGen, ez, false);
@@ -885,8 +885,7 @@ bool PuffAligner::alignRead(std::string& read, std::string& read_rc, const std::
                      -1 * mopts.gapExtendPenalty * readWindow.length());
           if (mopts.computeCIGAR) {
             if (allowSoftclip && remainedSoftClipLen >= 0) {
-              cigarGen.end_softclip_len = readWindow.length();
-              cigarGen.endOverhang = true;
+              cigarGen.add_item(readWindow.length(), 'S');
             } else {
               cigarGen.add_item(readWindow.length(), 'I');
             }