Changeset 3194

Timestamp:

Apr 22, 2014, 11:24:56 AM (9 years ago)

Author:

Peter

Message:

add missing file. see r3173

Location:

trunk

Files:

• test/bam_pair_iterator.cc (added)
• yat/utility/Aligner.cc (modified) (2 diffs)
• yat/utility/Aligner.h (modified) (3 diffs)

trunk/yat/utility/Aligner.cc

@@ -84 +84 @@
         if (x(i-1, j-1) + score(i-1, j-1) > x(i,j)) {
           x(i,j) = x(i-1, j-1) + score(i-1, j-1);
-          cigar(i, j) = diagonal;
+          directions(i, j) = diagonal;
         }
 
-        if (cigar(i, j-1) == right) {
+        if (directions(i, j-1) == right) {
           if (x(i, j-1)-horizon_gap_ > x(i,j)) {
             x(i,j) = x(i,j-1) - horizon_gap_;
-            cigar(i,j) = right;
+            directions(i,j) = right;
           }
         }
         else if(x(i,j-1)-horizon_gap_-open_horizon_gap_ > x(i,j)) {
           x(i,j) = x(i,j-1) - horizon_gap_ - open_horizon_gap_;
-          cigar(i,j) = right;
+          directions(i,j) = right;
         }
 
-        if (cigar(i-1,j) == down) {
+        if (directions(i-1,j) == down) {
           if (x(i-1,j) - vertical_gap_ > x(i,j)) {
             x(i,j) = x(i-1,j) - vertical_gap_;
-            cigar(i,j) = down;
+            directions(i,j) = down;
           }
         }
         else if (x(i-1,j) - vertical_gap_ - open_vertical_gap_ > x(i,j)) {
           x(i,j) = x(i-1,j) - vertical_gap_ - open_vertical_gap_;
-          cigar(i,j) = down;
+          directions(i,j) = down;
         }
       }
@@ -118 +118 @@
 
 
-  Aligner::direction& Aligner::cigar(size_t i, size_t j)
+  Aligner::direction& Aligner::directions(size_t i, size_t j)
   {
     return alignment_[i*columns_ + j];

trunk/yat/utility/Aligner.h

@@ -24 +24 @@
 */
 
+#include <boost/cstdint.hpp>
+
 #include <cstddef>
+#include <iosfwd>
 #include <vector>
 
@@ -126 +129 @@
     const direction& alignment(size_t i, size_t j) const;
 
+    /**
+       \since new in yat 0.12
+     */
+    class Cigar
+    {
+    public:
+      void clear(void);
+      void push_back(uint8_t op, uint32_t len=1);
+      void push_front(uint8_t op, uint32_t len=1);
+      void pop_back(void);
+      void pop_front(void);
+      uint8_t op(size_t) const;
+      char opchr(size_t) const;
+      uint32_t oplen(size_t) const;
+      uint32_t operator[](size_t) const;
+      size_t size(void) const;
+    private:
+      // using compiler generated copy
+      // Cigar(const Cigar& other);
+      // Cigar& operator=(const Cigar&);
+    };
+
+    /**
+       \since new in yat 0.12
+     */
+    const Cigar cigar(size_t i, size_t j) const;
+
   private:
-    direction& cigar(size_t i, size_t j);
+    direction& directions(size_t i, size_t j);
 
     size_t columns_;
@@ -137 +167 @@
   };
 
+
+  /**
+   */
+  std::ostream& operator<<(std::ostream& os, const Aligner::Cigar& cigar);
+
 }}} // of namespace utility, yat, and theplu