Fixed two bugs for very high scoring alignments

torognes · Jan 17, 2014 · 934a2d9 · 934a2d9 · torognes · Jan 17, 2014
1 parent d289979
commit 934a2d9
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Showing 8 changed files with 14 additions and 4 deletions.
diff --git a/CHANGES b/CHANGES
@@ -1,3 +1,12 @@
+2014-01-17  Torbjorn Rognes  <[email protected]>
+	* Version 2.0.8
+	* Removed a bug in computation of the score of alignments 
+	  with a score higher than 32767
+	* Removed a bug in computation of the alignment of sequences
+	  that scored higher than 65535
+	* No Mac executable this time, but coming soon (need to adapt
+	  inline assembler syntax to the LLVM clang compiler)
+
 2013-05-02  Torbjorn Rognes  <[email protected]>
 	* Version 2.0.7
 	* Removed a few memory leaks discovered with Valgrind

diff --git a/Linux/mpiswipe b/Linux/mpiswipe
diff --git a/Linux/swipe b/Linux/swipe
diff --git a/Mac/swipe b/Mac/swipe
diff --git a/search16.cc b/search16.cc
@@ -457,7 +457,7 @@ void search16(WORD * * q_start,
 
 	  if (cand_id >= 0)
 	  {
-	    long score = ((WORD*)&S)[c] - 0x8000;
+	    long score = ((WORD*)&S)[c] ^ 0x8000;
 	    scores[cand_id] = score;
 	    bestpos[cand_id] = d_best[c] - d_begin[c];
 	    done++;

diff --git a/search16s.cc b/search16s.cc
@@ -445,7 +445,7 @@ void search16s(WORD * * q_start,
 
 	  if (cand_id >= 0)
 	  {
-	    long score = ((WORD*)&S)[c] - 0x8000;
+	    long score = ((WORD*)&S)[c] ^ 0x8000;
 	    scores[cand_id] = score;
 	    bestpos[cand_id] = d_best[c] - d_begin[c];	    
 	    bestq[cand_id] = q_best[c];

diff --git a/swipe.cc b/swipe.cc
@@ -401,7 +401,8 @@ void align_chunk(struct search_data * sdp, long hitfirst, long hitlast)
 
 	    long hitno = sdp->start_hits[i];
 
-	    hits_enter_align_hint(hitno, bestq, pos);
+	    if (sdp->scores[i] < SCORELIMIT_16)
+	      hits_enter_align_hint(hitno, bestq, pos);
 	  }
 	}
       }

diff --git a/swipe.h b/swipe.h
@@ -55,7 +55,7 @@
 #define LINE_MAX 2048
 #endif
 
-#define SWIPE_VERSION "2.0.7"
+#define SWIPE_VERSION "2.0.8"
 
 // Should be 32bits integer
 typedef unsigned int UINT32;