Fix issue #24; add a preliminary implementation of seqdiff

veg · Jul 18, 2022 · 5448fac · 5448fac
1 parent 3c80030
commit 5448fac
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Showing 3 changed files with 7 additions and 9 deletions.
diff --git a/VERSION.txt b/VERSION.txt
@@ -1 +1 @@
-v1.0.8
+v1.0.9
diff --git a/src/seqdiff.cpp b/src/seqdiff.cpp
@@ -112,8 +112,8 @@ int main(int argc, const char *argv[]) {
                   "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b"
                   "\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bProgress"
                   ":"
-               << setw(8) << percentDone << "% " << setw(12) << std::setprecision(3)
-               << seq_id / difftime(after, before) << " evals/sec)";
+               << setw(8) << percentDone << "% (" << setw(12) << std::setprecision(3)
+               << seq_id / difftime(after, before) << " seqs/sec)";
 
           after = before;
         }

diff --git a/src/tn93_shared.cc b/src/tn93_shared.cc
@@ -588,19 +588,17 @@ double		computeTN93 (const char * __restrict__ s1, const char * __restrict__ s2,
             if (__builtin_expect(c1 < 4 && c2 < 4, 1)) {
               integer_counts [c1][c2] ++;
             } else { // not both resolved
-              if (c1 == GAP || c2 == GAP) {
-                continue;
+              if (c1 != GAP && c2 != GAP) {
+                ambiguityHandler (c1,c2);
               }
-              ambiguityHandler (c1,c2);
             }
 
             if (__builtin_expect(c3 < 4 && c4 < 4, 1)) {
               integer_counts2 [c3][c4] ++;
             } else { // not both resolved
-              if (c3 == GAP || c4 == GAP) {
-                continue;
+              if (c3 != GAP && c4 != GAP) {
+                ambiguityHandler (c3,c4);
               }
-              ambiguityHandler (c3,c4);
             }
         }