[med-svn] [Git][med-team/daligner][upstream] New upstream version 1.0+git20230620.f9a35a8

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / daligner


Commits:
2a05ca53 by Étienne Mollier at 2023-07-20T11:05:37+02:00
New upstream version 1.0+git20230620.f9a35a8
- - - - -


2 changed files:

- LAsort.c
- align.c


Changes:

=====================================
LAsort.c
=====================================
@@ -241,7 +241,7 @@ int main(int argc, char *argv[])
   for (i = 1; i < argc; i++)
     { int64    *perm;
       FILE     *input, *foutput;
-      int64     novl, sov;
+      int64     novl, sov, bovl;
       Block_Looper *parse;
 
       parse = Parse_Block_LAS_Arg(argv[i]);
@@ -273,9 +273,9 @@ int main(int argc, char *argv[])
             if (VERBOSE)
               { printf("  %s: ",root);
                 Print_Number(novl,0,stdout);
-                printf(" records ");
+                printf(" records, ");
                 Print_Number(size-novl*ovlsize,0,stdout);
-                printf(" trace bytes\n");
+                printf(" trace bytes");
                 fflush(stdout);
               }
 
@@ -361,6 +361,7 @@ int main(int argc, char *argv[])
             y.aread = ((Overlap *) (iblock+perm[0]))->aread+1;
             x = &y;
 
+            bovl = novl;
             fptr = fblock;
             ftop = fblock + osize;
             for (j = 0; j < sov; j++)
@@ -375,9 +376,7 @@ int main(int argc, char *argv[])
                         fptr = fblock;
                       }
                     if (equal)
-                      { fptr += (ovlsize + tsize);
-                        novl -= 1;
-                      }
+                      novl -= 1;
                     else
                       { memmove(fptr,((char *) w)+ptrsize,ovlsize);
                         fptr += ovlsize;
@@ -399,6 +398,16 @@ int main(int argc, char *argv[])
           if (fwrite(&novl,sizeof(int64),1,foutput) != 1)
             SYSTEM_WRITE_ERROR
 
+          if (VERBOSE)
+            { if (bovl == novl)
+                fprintf(stdout,"\n");
+              else
+                { fprintf(stdout,", ");
+                  Print_Number(bovl-novl,0,stdout);
+                  fprintf(stdout," duplicates removed\n");
+                }
+            }
+
           free(perm);
           fclose(foutput);
         }


=====================================
align.c
=====================================
@@ -5155,6 +5155,8 @@ int Compute_Trace_PTS(Alignment *align, Work_Data *ework, int trace_spacing, int
       }
     if (tlen <= 1)
       nmax = N;
+    if (dmax & 0x1)
+      dmax += 1;
 
     s = (dmax+3)*2*((trace_spacing+nmax+3)*sizeof(int) + sizeof(int *));
 
@@ -5265,6 +5267,8 @@ int Compute_Trace_MID(Alignment *align, Work_Data *ework, int trace_spacing, int
       }
     if (tlen <= 1)
       nmax = N;
+    if (dmax & 0x1)
+      dmax += 1;
 
     s = (dmax+3)*4*((trace_spacing+nmax+3)*sizeof(int) + sizeof(int *));
 



View it on GitLab: https://salsa.debian.org/med-team/daligner/-/commit/2a05ca53bddcc931a445b46846ef1832ee099571

-- 
View it on GitLab: https://salsa.debian.org/med-team/daligner/-/commit/2a05ca53bddcc931a445b46846ef1832ee099571
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