diff options
| -rw-r--r-- | LAsort.c | 21 | ||||
| -rw-r--r-- | ONE2LA.c | 2 | ||||
| -rw-r--r-- | QV.c | 2 | ||||
| -rw-r--r-- | align.c | 4 | ||||
| -rw-r--r-- | debian/changelog | 7 | ||||
| -rw-r--r-- | debian/patches/typos.patch | 24 |
6 files changed, 51 insertions, 9 deletions
@@ -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); } @@ -152,7 +152,7 @@ int main(int argc, char *argv[]) { 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') @@ -1319,7 +1319,7 @@ error: 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) @@ -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 *)); diff --git a/debian/changelog b/debian/changelog index 84a5049..effa539 100644 --- a/debian/changelog +++ b/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@debian.org> Thu, 20 Jul 2023 11:10:34 +0200 + daligner (1.0+git20221215.bd26967-1) unstable; urgency=medium * New upstream version diff --git a/debian/patches/typos.patch b/debian/patches/typos.patch index 93fc1b7..5549025 100644 --- a/debian/patches/typos.patch +++ b/debian/patches/typos.patch @@ -1,7 +1,7 @@ Description: fix a couple of typos caught by lintian. Author: Étienne Mollier <emollier@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) |