[med-svn] [Git][med-team/daligner][master] 8 commits: routine-update: New upstream version
Steffen Möller
gitlab at salsa.debian.org
Sat Jun 13 14:38:58 BST 2020
Steffen Möller pushed to branch master at Debian Med / daligner
Commits:
15e4b1cd by Steffen Moeller at 2020-06-13T15:37:20+02:00
routine-update: New upstream version
- - - - -
2d72004d by Steffen Moeller at 2020-06-13T15:37:21+02:00
New upstream version 1.0+git20200608.c18a2fb
- - - - -
2e3f6107 by Steffen Moeller at 2020-06-13T15:37:21+02:00
Update upstream source from tag 'upstream/1.0+git20200608.c18a2fb'
Update to upstream version '1.0+git20200608.c18a2fb'
with Debian dir e003ef4027b8105b1acb0393e3f12b0c24a2dd0e
- - - - -
782d123a by Steffen Moeller at 2020-06-13T15:37:21+02:00
routine-update: debhelper-compat 13
- - - - -
04389e1e by Steffen Moeller at 2020-06-13T15:37:24+02:00
routine-update: Add salsa-ci file
- - - - -
c575951d by Steffen Moeller at 2020-06-13T15:37:24+02:00
routine-update: Rules-Requires-Root: no
- - - - -
fca63077 by Steffen Moeller at 2020-06-13T15:37:29+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
22da4fbc by Steffen Moeller at 2020-06-13T15:37:58+02:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- DB.c
- LAsort.c
- LAsplit.c
- daligner.c
- debian/changelog
- debian/control
- + debian/salsa-ci.yml
- debian/upstream/metadata
Changes:
=====================================
DB.c
=====================================
@@ -1758,7 +1758,6 @@ static int Late_Track_Trim(DAZZ_DB *db, DAZZ_TRACK *track, int ispart)
j += 1;
}
}
- track->data = Realloc(track->data,anno4[j],NULL);
track->alen = Realloc(track->alen,sizeof(int)*j,NULL);
track->anno = Realloc(track->anno,track->size*(j+1),NULL);
}
@@ -1779,7 +1778,6 @@ static int Late_Track_Trim(DAZZ_DB *db, DAZZ_TRACK *track, int ispart)
j += 1;
}
}
- track->data = Realloc(track->data,anno8[j],NULL);
track->alen = Realloc(track->alen,sizeof(int)*j,NULL);
track->anno = Realloc(track->anno,track->size*(j+1),NULL);
}
=====================================
LAsort.c
=====================================
@@ -58,6 +58,26 @@ static int SORT_OVL(const void *x, const void *y)
if (pl != pr)
return (pl-pr);
+ pl = ol->path.aepos;
+ pr = or->path.aepos;
+ if (pl != pr)
+ return (pl-pr);
+
+ pl = ol->path.bbpos;
+ pr = or->path.bbpos;
+ if (pl != pr)
+ return (pl-pr);
+
+ pl = ol->path.bepos;
+ pr = or->path.bepos;
+ if (pl != pr)
+ return (pl-pr);
+
+ pl = ol->path.diffs;
+ pr = or->path.diffs;
+ if (pl != pr)
+ return (pl-pr);
+
if (ol < or)
return (-1);
else if (ol > or)
@@ -72,6 +92,8 @@ static int SORT_MAP(const void *x, const void *y)
Overlap *ol, *or;
int al, ar;
+ int bl, br;
+ int cl, cr;
int pl, pr;
ol = (Overlap *) (IBLOCK+l);
@@ -87,6 +109,36 @@ static int SORT_MAP(const void *x, const void *y)
if (pl != pr)
return (pl-pr);
+ bl = ol->bread;
+ br = or->bread;
+ if (bl != br)
+ return (bl-br);
+
+ cl = COMP(ol->flags);
+ cr = COMP(or->flags);
+ if (cl != cr)
+ return (cl-cr);
+
+ pl = ol->path.aepos;
+ pr = or->path.aepos;
+ if (pl != pr)
+ return (pl-pr);
+
+ pl = ol->path.bbpos;
+ pr = or->path.bbpos;
+ if (pl != pr)
+ return (pl-pr);
+
+ pl = ol->path.bepos;
+ pr = or->path.bepos;
+ if (pl != pr)
+ return (pl-pr);
+
+ pl = ol->path.diffs;
+ pr = or->path.diffs;
+ if (pl != pr)
+ return (pl-pr);
+
if (ol < or)
return (-1);
else if (ol > or)
@@ -95,6 +147,50 @@ static int SORT_MAP(const void *x, const void *y)
return (0);
}
+static int EQUAL(Overlap *ol, Overlap *or)
+{ int al, ar;
+ int bl, br;
+ int cl, cr;
+ int pl, pr;
+
+ al = ol->aread;
+ ar = or->aread;
+ if (al != ar)
+ return (0);
+
+ bl = ol->bread;
+ br = or->bread;
+ if (bl != br)
+ return (0);
+
+ cl = COMP(ol->flags);
+ cr = COMP(or->flags);
+ if (cl != cr)
+ return (0);
+
+ pl = ol->path.abpos;
+ pr = or->path.abpos;
+ if (pl != pr)
+ return (0);
+
+ pl = ol->path.aepos;
+ pr = or->path.aepos;
+ if (pl != pr)
+ return (0);
+
+ pl = ol->path.bbpos;
+ pr = or->path.bbpos;
+ if (pl != pr)
+ return (0);
+
+ pl = ol->path.bepos;
+ pr = or->path.bepos;
+ if (pl != pr)
+ return (0);
+
+ return (1);
+}
+
int main(int argc, char *argv[])
{ char *iblock, *fblock, *iend;
int64 isize, osize;
@@ -249,30 +345,39 @@ int main(int argc, char *argv[])
qsort(perm,sov,sizeof(int64),SORT_MAP);
else
qsort(perm,sov,sizeof(int64),SORT_OVL);
-
+
// Output the records in sorted order
- { int j;
- Overlap *w;
+ { int j, equal;
+ Overlap *w, *x, y;
int64 tsize, span;
char *fptr, *ftop, *wo;
+ y.aread = ((Overlap *) (iblock+perm[0]))->aread+1;
+ x = &y;
+
fptr = fblock;
ftop = fblock + osize;
for (j = 0; j < sov; j++)
{ w = (Overlap *) (wo = iblock+perm[j]);
do
- { tsize = w->path.tlen*tbytes;
+ { equal = EQUAL(w,x);
+ tsize = w->path.tlen*tbytes;
span = ovlsize + tsize;
if (fptr + span > ftop)
{ if (fwrite(fblock,1,fptr-fblock,foutput) != (size_t) (fptr-fblock))
SYSTEM_WRITE_ERROR
fptr = fblock;
}
- memmove(fptr,((char *) w)+ptrsize,ovlsize);
- fptr += ovlsize;
- memmove(fptr,(char *) (w+1),tsize);
- fptr += tsize;
+ if (equal)
+ fptr += (ovlsize + tsize);
+ else
+ { memmove(fptr,((char *) w)+ptrsize,ovlsize);
+ fptr += ovlsize;
+ memmove(fptr,(char *) (w+1),tsize);
+ fptr += tsize;
+ }
+ x = w;
w = (Overlap *) (wo += span);
}
while (wo < iend && CHAIN_NEXT(w->flags));
=====================================
LAsplit.c
=====================================
@@ -64,14 +64,16 @@ int main(int argc, char *argv[])
parts = strtol(argv[2],&eptr,10);
if (*eptr != '\0')
- { pwd = PathTo(argv[2]);
+ { pwd = PathTo(argv[2]);
if (strcmp(argv[2]+(strlen(argv[2])-4),".dam") == 0)
{ root = Root(argv[2],".dam");
stub = Read_DB_Stub(Catenate(pwd,"/",root,".dam"),DB_STUB_BLOCKS);
+ parts = stub->nblocks;
}
else
{ root = Root(argv[2],".db");
stub = Read_DB_Stub(Catenate(pwd,"/",root,".db"),DB_STUB_BLOCKS);
+ parts = stub->nblocks;
}
free(pwd);
free(root);
@@ -173,7 +175,7 @@ int main(int argc, char *argv[])
last = w->aread;
}
else
- { if (w->aread > last)
+ { if (w->aread >= last)
break;
}
=====================================
daligner.c
=====================================
@@ -51,8 +51,8 @@
#include "filter.h"
static char *Usage[] =
- { "[-vaABI] [-k<int(16)>] [-%<int(28)>] [-h<int(50)>] [-w<int(6)>] [-t<int>] [-M<int>]",
- " [-e<double(.75)] [-l<int(1500)>] [-s<int(100)>] [-H<int>]",
+ { "[-vaABI] [-k<int(16)>] [-%<int(28)>] [-h<int(50)>] [-w<int(6)>] [-t<int>]",
+ " [-M<int>] [-e<double(.75)] [-l<int(1500)>] [-s<int(100)>] [-H<int>]",
" [-T<int(4)>] [-P<dir(/tmp)>] [-m<track>]+",
" <subject:db|dam> <target:db|dam> ...",
};
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+daligner (1.0+git20200608.c18a2fb-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * debhelper-compat 13 (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit.
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 13 Jun 2020 15:37:29 +0200
+
daligner (1.0+git20200115.c2b47da-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -3,11 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12)
+Build-Depends: debhelper-compat (= 13)
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/daligner
Vcs-Git: https://salsa.debian.org/med-team/daligner.git
Homepage: https://dazzlerblog.wordpress.com
+Rules-Requires-Root: no
Package: daligner
Architecture: any
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/thegenemyers/DALIGNER/issues
+Bug-Submit: https://github.com/thegenemyers/DALIGNER/issues/new
Reference:
Author: Gene Myers
Title: Efficient Local Alignment Discovery amongst Noisy Long Reads
View it on GitLab: https://salsa.debian.org/med-team/daligner/-/compare/76cae0e0174311ec2c41e85844df29320b9a4009...22da4fbc92b54b6cf56a59527583fc47165ab02b
--
View it on GitLab: https://salsa.debian.org/med-team/daligner/-/compare/76cae0e0174311ec2c41e85844df29320b9a4009...22da4fbc92b54b6cf56a59527583fc47165ab02b
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