Merge pull request #259 from waveygang/multi-patch

Multi-patch

src/common/wflign/src/wflign_alignment.cpp

@@ -87,6 +87,23 @@ alignment_t& alignment_t::operator=(alignment_t&& other) noexcept {
     return *this;
 }
 
+int alignment_t::query_begin() {
+    return j;
+}
+
+int alignment_t::query_end() {
+    return j + query_length;
+}
+
+int alignment_t::target_begin() {
+    return i;
+}
+
+int alignment_t::target_end() {
+    return i + target_length;
+}
+
+
 //void alignment_t::display(void) {
 //    std::cerr << j << " " << i << " " << query_length << " "
 //              << target_length << " " << ok << std::endl;

src/common/wflign/src/wflign_alignment.hpp

@@ -37,6 +37,7 @@ class alignment_t {
     int target_length;
     bool ok;
     bool keep;
+    bool is_rev;
     wflign_cigar_t edit_cigar;
     // Default constructor
     alignment_t();
@@ -53,6 +54,12 @@ class alignment_t {
     // Trim functions
     void trim_front(int query_trim);
     void trim_back(int query_trim);
+    // query_begin, query_end, target_begin, target_end
+    // Accessors
+    int query_begin();
+    int query_end();
+    int target_begin();
+    int target_end();
 };