[med-svn] [Git][med-team/daligner][master] 4 commits: routine-update: New upstream version
Steffen Möller
gitlab at salsa.debian.org
Mon Aug 10 15:02:52 BST 2020
Steffen Möller pushed to branch master at Debian Med / daligner
Commits:
5aeb3bc2 by Steffen Moeller at 2020-08-10T16:01:39+02:00
routine-update: New upstream version
- - - - -
02bb795f by Steffen Moeller at 2020-08-10T16:01:40+02:00
New upstream version 1.0+git20200727.ed40ce5
- - - - -
2eca2fe1 by Steffen Moeller at 2020-08-10T16:01:40+02:00
Update upstream source from tag 'upstream/1.0+git20200727.ed40ce5'
Update to upstream version '1.0+git20200727.ed40ce5'
with Debian dir c0af25f3b8538f6b1e515b775e583ab842a8e70d
- - - - -
d21f1ee2 by Steffen Moeller at 2020-08-10T16:02:33+02:00
routine-update: Ready to upload to unstable
- - - - -
5 changed files:
- LAsort.c
- daligner.c
- debian/changelog
- filter.c
- filter.h
Changes:
=====================================
LAsort.c
=====================================
@@ -284,10 +284,10 @@ int main(int argc, char *argv[])
exit (1);
if (fwrite(&novl,sizeof(int64),1,foutput) != 1)
- SYSTEM_READ_ERROR
+ SYSTEM_WRITE_ERROR
if (fwrite(&tspace,sizeof(int),1,foutput) != 1)
- SYSTEM_READ_ERROR
-
+ SYSTEM_WRITE_ERROR
+
if (size > isize)
{ if (iblock == NULL)
iblock = Malloc(size+ptrsize,"Allocating LAsort input block");
@@ -309,6 +309,11 @@ int main(int argc, char *argv[])
free(root);
free(path);
}
+
+ if (novl == 0)
+ { fclose(foutput);
+ continue;
+ }
// Set up unsorted permutation array
@@ -337,7 +342,7 @@ int main(int argc, char *argv[])
sov = novl;
}
}
-
+
// Sort permutation array of ptrs to records
IBLOCK = iblock;
@@ -370,7 +375,9 @@ int main(int argc, char *argv[])
fptr = fblock;
}
if (equal)
- fptr += (ovlsize + tsize);
+ { fptr += (ovlsize + tsize);
+ novl -= 1;
+ }
else
{ memmove(fptr,((char *) w)+ptrsize,ovlsize);
fptr += ovlsize;
@@ -388,12 +395,15 @@ int main(int argc, char *argv[])
}
}
+ rewind(foutput);
+ if (fwrite(&novl,sizeof(int64),1,foutput) != 1)
+ SYSTEM_WRITE_ERROR
+
free(perm);
fclose(foutput);
}
Free_Block_Arg(parse);
}
-
if (iblock != NULL)
free(iblock - ptrsize);
=====================================
daligner.c
=====================================
@@ -40,6 +40,7 @@
#include <sys/types.h>
#include <sys/stat.h>
#include <dirent.h>
+#include <sys/resource.h>
#include <sys/param.h>
#if defined(BSD)
@@ -470,6 +471,12 @@ int main(int argc, char *argv[])
int NTHREADS;
int MAP_ORDER;
+#ifdef PROFILE
+ struct rusage stime, etime;
+
+ getrusage(RUSAGE_SELF, &stime);
+#endif
+
{ int i, j, k;
int flags[128];
char *eptr;
@@ -728,7 +735,24 @@ int main(int argc, char *argv[])
Close_DB(ablock);
free(apath);
free(aroot);
- Clean_Exit(0);
+#ifdef PROFILE
+ { int64 secs, mics;
+
+ getrusage(RUSAGE_SELF, &etime);
+
+ secs = etime.ru_utime.tv_sec - stime.ru_utime.tv_sec;
+ mics = etime.ru_utime.tv_usec - stime.ru_utime.tv_usec;
+ mics += 1000000*secs;
+
+ secs = etime.ru_stime.tv_sec - stime.ru_stime.tv_sec;
+ mics += etime.ru_stime.tv_usec - stime.ru_stime.tv_usec;
+ mics += 1000000*secs;
+
+ printf("T %lld\n",mics/1000);
+ }
+#endif
+
+ Clean_Exit(0);
exit (0);
}
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+daligner (1.0+git20200727.ed40ce5-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 10 Aug 2020 16:01:48 +0200
+
daligner (1.0+git20200608.c18a2fb-1) unstable; urgency=medium
* Team upload.
=====================================
filter.c
=====================================
@@ -28,7 +28,7 @@
#include "filter.h"
#include "align.h"
-#undef PROFILE // WHen running sensitivity trials, compute histogram of
+ // WHen running sensitivity trials, compute histogram of
#define MAXHIT 1000 // false & true positive hit scores
// Debug Controls
@@ -2521,7 +2521,7 @@ void Match_Filter(char *aname, DAZZ_DB *ablock, char *bname, DAZZ_DB *bblock,
}
#endif
- { int max_diag = ((ablock->maxlen >> Binshift) - ((-bblock->maxlen) >> Binshift)) + 1;
+ { int max_diag = ((ablock->maxlen >> Binshift) - ((-bblock->maxlen) >> Binshift)) + 3;
int *space;
int i;
@@ -2556,7 +2556,7 @@ void Match_Filter(char *aname, DAZZ_DB *ablock, char *bname, DAZZ_DB *bblock,
space[i] = 0;
for (i = 0; i < NTHREADS; i++)
{ if (i == 0)
- parmr[i].score = space - ((-bblock->maxlen) >> Binshift);
+ parmr[i].score = space - (((-bblock->maxlen) >> Binshift) - 1);
else
parmr[i].score = parmr[i-1].lasta + max_diag;
parmr[i].lastp = parmr[i].score + max_diag;
=====================================
filter.h
=====================================
@@ -14,6 +14,8 @@
#include "DB.h"
#include "align.h"
+#undef PROFILE
+
extern int VERBOSE; // -v flag is set?
extern int MINOVER; // minimum overlap (-l)
extern int HGAP_MIN; // HGap minimum (-H)
View it on GitLab: https://salsa.debian.org/med-team/daligner/-/compare/22da4fbc92b54b6cf56a59527583fc47165ab02b...d21f1ee257a2ce3982a84e44c3c8a9f63b33b921
--
View it on GitLab: https://salsa.debian.org/med-team/daligner/-/compare/22da4fbc92b54b6cf56a59527583fc47165ab02b...d21f1ee257a2ce3982a84e44c3c8a9f63b33b921
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