make s_align.flag as the return value of c++ API Align function

Author: Mengyao Zhao

src/example.cpp

@@ -5,7 +5,7 @@
 // 1) g++ -Wall ssw_cpp.cpp ssw.c example.cpp
 // 2) ./a.out
 // Created by Wan-Ping Lee on 09/04/12.
-// Last revision by Mengyao Zhao on 2017-06-05
+// Last revision by Mengyao Zhao on 2023-Apr-21
 // ==========================
 
 #include <iostream>
@@ -24,8 +24,6 @@ int main() {
   const string query = "CTGAGCCGGTAAATC";
   int32_t maskLen = strlen(query.c_str())/2;
   maskLen = maskLen < 15 ? 15 : maskLen;
-  //const string ref   = "CCGTTTATCGCA";
-  //const string query = "CCTTTTATCGCA";
 
   // Declares a default Aligner
   StripedSmithWaterman::Aligner aligner;

src/ssw.c

@@ -56,7 +56,7 @@
  *
  *  Created by Mengyao Zhao on 6/22/10.
  *  Copyright 2010 Boston College. All rights reserved.
- *	Version 1.2.4
+ *	Version 1.2.5
  *	Last revision by Mengyao Zhao on 2022-Apr-17.
  *
  *  The lazy-F loop implementation was derived from SWPS3, which is

src/ssw_cpp.cpp

@@ -1,6 +1,6 @@
 // ssw_cpp.cpp
 // Created by Wan-Ping Lee
-// Last revision by Mengyao Zhao on 2017-05-30
+// Last revision by Mengyao Zhao on 2023-Apr-21
 
 #include "ssw_cpp.h"
 #include "ssw.h"
@@ -290,25 +290,18 @@ int Aligner::SetReferenceSequence(const char* seq, const int& length) {
 
   int len = 0;
   if (translation_matrix_) {
-    // calculate the valid length
-    //int calculated_ref_length = static_cast<int>(strlen(seq));
-    //int valid_length = (calculated_ref_length > length)
-    //                   ? length : calculated_ref_length;
-    int valid_length = length;
     // delete the current buffer
     CleanReferenceSequence();
     // allocate a new buffer
-    translated_reference_ = new int8_t[valid_length];
+    translated_reference_ = new int8_t[length];
 
-    len = TranslateBase(seq, valid_length, translated_reference_);
+    len = TranslateBase(seq, length, translated_reference_);
   } else {
     // nothing
   }
 
   reference_length_ = len;
   return len;
-
-
 }
 
 int Aligner::TranslateBase(const char* bases, const int& length,
@@ -326,7 +319,7 @@ int Aligner::TranslateBase(const char* bases, const int& length,
 }
 
 
-bool Aligner::Align(const char* query, const Filter& filter,
+uint16_t Aligner::Align(const char* query, const Filter& filter,
                     Alignment* alignment, const int32_t maskLen) const
 {
   if (!translation_matrix_) return false;
@@ -351,18 +344,18 @@ bool Aligner::Align(const char* query, const Filter& filter,
   alignment->Clear();
   ConvertAlignment(*s_al, query_len, alignment);
   alignment->mismatches = CalculateNumberMismatch(&*alignment, translated_reference_, translated_query, query_len);
-
+  uint16_t align_flag = s_al->flag;
 
   // Free memory
   delete [] translated_query;
   align_destroy(s_al);
   init_destroy(profile);
 
-  return true;
+  return align_flag;
 }
 
 
-bool Aligner::Align(const char* query, const char* ref, const int& ref_len,
+uint16_t Aligner::Align(const char* query, const char* ref, const int& ref_len,
                     const Filter& filter, Alignment* alignment, const int32_t maskLen) const
 {
   if (!translation_matrix_) return false;
@@ -392,14 +385,15 @@ bool Aligner::Align(const char* query, const char* ref, const int& ref_len,
   alignment->Clear();
   ConvertAlignment(*s_al, query_len, alignment);
   alignment->mismatches = CalculateNumberMismatch(&*alignment, translated_ref, translated_query, query_len);
+  uint16_t align_flag = s_al->flag;
 
   // Free memory
   delete [] translated_query;
   delete [] translated_ref;
   align_destroy(s_al);
   init_destroy(profile);
 
-  return true;
+  return align_flag;
 }
 
 void Aligner::Clear(void) {

src/ssw_cpp.h

@@ -1,6 +1,6 @@
 // ssw_cpp.h
 // Created by Wan-Ping Lee
-// Last revision by Mengyao Zhao on 2017-05-30
+// Last revision by Mengyao Zhao on 2023-Apr-21
 
 #ifndef COMPLETE_STRIPED_SMITH_WATERMAN_CPP_H_
 #define COMPLETE_STRIPED_SMITH_WATERMAN_CPP_H_
@@ -109,7 +109,7 @@ class Aligner {
   //                    and replaced.
   // @param    seq    The reference bases;
   //                  [NOTICE] It is not necessary null terminated.
-  // @param    length The length of bases will be be built.
+  // @param    length The length of bases will be built.
   // @return   The length of the built bases.
   // =========
   int SetReferenceSequence(const char* seq, const int& length);
@@ -134,9 +134,9 @@ class Aligner {
   // @param    maskLen   The distance between the optimal and suboptimal alignment ending position will >= maskLen. We suggest to 
   //                     use readLen/2, if you don't have special concerns. Note: maskLen has to be >= 15, otherwise this function 
   //                     will NOT return the suboptimal alignment information.
-  // @return   True: succeed; false: fail.
+  // @return   If the alignment path is accurate (or has missing part). 0: accurate; 1: banded_sw is totally failed; 2: banded_sw returned path has missing part
   // =========
-  bool Align(const char* query, const Filter& filter, Alignment* alignment, const int32_t maskLen) const;
+  uint16_t Align(const char* query, const Filter& filter, Alignment* alignment, const int32_t maskLen) const;
 
   // =========
   // @function Align the query againt the reference.
@@ -151,9 +151,9 @@ class Aligner {
   // @param    maskLen   The distance between the optimal and suboptimal alignment ending position will >= maskLen. We suggest to 
   //                     use readLen/2, if you don't have special concerns. Note: maskLen has to be >= 15, otherwise this function 
   //                     will NOT return the suboptimal alignment information.
-  // @return   True: succeed; false: fail.
+  // @return   If the alignment path is accurate (or has missing part). 0: accurate; 1: banded_sw is totally failed; 2: banded_sw returned path has missing part
   // =========
-  bool Align(const char* query, const char* ref, const int& ref_len,
+  uint16_t Align(const char* query, const char* ref, const int& ref_len,
              const Filter& filter, Alignment* alignment, const int32_t maskLen) const;
 
   // @function Clear up all containers and thus the aligner is disabled.