[med-svn] [Git][med-team/daligner][master] 5 commits: routine-update: New upstream version

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / daligner


Commits:
749e1a29 by Étienne Mollier at 2023-07-20T11:05:36+02:00
routine-update: New upstream version

- - - - -
2a05ca53 by Étienne Mollier at 2023-07-20T11:05:37+02:00
New upstream version 1.0+git20230620.f9a35a8
- - - - -
409986d8 by Étienne Mollier at 2023-07-20T11:05:37+02:00
Update upstream source from tag 'upstream/1.0+git20230620.f9a35a8'

Update to upstream version '1.0+git20230620.f9a35a8'
with Debian dir a0a91c98078dbc96bce7b126e3bfb24ef5505d13
- - - - -
a9fa6b73 by Étienne Mollier at 2023-07-20T11:09:20+02:00
typos.patch: fix "auxiliary" typos.

- - - - -
f3b985d7 by Étienne Mollier at 2023-07-20T11:10:48+02:00
ready to upload to unstable.

- - - - -


4 changed files:

- LAsort.c
- align.c
- debian/changelog
- debian/patches/typos.patch


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 *));
 


=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+daligner (1.0+git20230620.f9a35a8-1) unstable; urgency=medium
+
+  * New upstream version 1.0+git20230620.f9a35a8
+  * typos.patch: fix "auxiliary" typos.
+
+ -- Étienne Mollier <emollier at debian.org>  Thu, 20 Jul 2023 11:10:34 +0200
+
 daligner (1.0+git20221215.bd26967-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/patches/typos.patch
=====================================
@@ -1,7 +1,7 @@
 Description: fix a couple of typos caught by lintian.
 Author: Étienne Mollier <emollier at debian.org>
 Forwarded: no
-Last-Update: 2022-08-03
+Last-Update: 2023-07-20
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- daligner.orig/DB.c
@@ -57,3 +57,25 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
              break;
            case 'H':
              ARG_POSITIVE(HGAP_MIN,"HGAP threshold (in bp.s)")
+--- daligner.orig/ONE2LA.c
++++ daligner/ONE2LA.c
+@@ -152,7 +152,7 @@
+         { t = oneReadLine(file1);
+ 
+           if (t == 0)
+-            { fprintf(stderr,"ONE2LA: Pile object not followed by sufficient auxilliary lines\n");
++            { fprintf(stderr,"ONE2LA: Pile object not followed by sufficient auxiliary lines\n");
+               exit (1);
+             }
+           if (has[t] > 0 && t != 'T' && t != 'Q')
+--- daligner.orig/QV.c
++++ daligner/QV.c
+@@ -1319,7 +1319,7 @@
+   EXIT(NULL);
+ }
+ 
+-  //  Free all the auxilliary storage associated with the encoding argument
++  //  Free all the auxiliary storage associated with the encoding argument
+ 
+ void Free_QVcoding(QVcoding *coding)
+ { if (coding->subChar >= 0)



View it on GitLab: https://salsa.debian.org/med-team/daligner/-/compare/7c207fe98a6868d1fd43fb46d32c86f3755c2a36...f3b985d7f529118c592576dd36926f553c8cc845

-- 
View it on GitLab: https://salsa.debian.org/med-team/daligner/-/compare/7c207fe98a6868d1fd43fb46d32c86f3755c2a36...f3b985d7f529118c592576dd36926f553c8cc845
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