[med-svn] [Git][med-team/lighter][master] 5 commits: New upstream version 1.1.3

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / lighter


Commits:
ded63b6f by Étienne Mollier at 2024-11-09T20:01:07+01:00
New upstream version 1.1.3
- - - - -
1c5785d2 by Étienne Mollier at 2024-11-09T20:01:19+01:00
Update upstream source from tag 'upstream/1.1.3'

Update to upstream version '1.1.3'
with Debian dir af46b8826c02a4abf38ebfde983dfcf9d962488a
- - - - -
c859c52e by Étienne Mollier at 2024-11-09T20:09:41+01:00
ftbfs.patch: unfuzz.

- - - - -
3297e2c2 by Étienne Mollier at 2024-11-09T20:10:24+01:00
d/control: declare compliance to standards version 4.7.0.

- - - - -
f1302a48 by Étienne Mollier at 2024-11-09T20:11:29+01:00
d/changelog: ready for upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/patches/ftbfs.patch
- main.cpp


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+lighter (1.1.3-1) unstable; urgency=medium
+
+  * New upstream version 1.1.3
+  * ftbfs.patch: unfuzz.
+  * d/control: declare compliance to standards version 4.7.0.
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 09 Nov 2024 20:11:20 +0100
+
 lighter (1.1.2-7) unstable; urgency=medium
 
   * Fix watch file


=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                zlib1g-dev
-Standards-Version: 4.6.1
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/lighter
 Vcs-Git: https://salsa.debian.org/med-team/lighter.git
 Homepage: https://github.com/mourisl/Lighter


=====================================
debian/patches/ftbfs.patch
=====================================
@@ -11,19 +11,19 @@ Description: lighter fails to build from source, because:
  and 3). A very simple fix is using signed char (which isn't architecture
  dependent).
 
---- lighter-1.1.2.orig/main.cpp
-+++ lighter-1.1.2/main.cpp
+--- lighter.orig/main.cpp
++++ lighter/main.cpp
 @@ -20,7 +20,7 @@
  
- char LIGHTER_VERSION[] = "Lighter v1.1.2" ;
+ char LIGHTER_VERSION[] = "Lighter v1.1.3" ;
  
 -char nucToNum[26] = { 0, -1, 1, -1, -1, -1, 2, 
 +signed char nucToNum[26] = { 0, -1, 1, -1, -1, -1, 2, 
  	-1, -1, -1, -1, -1, -1, -1,
  	-1, -1, -1, -1, -1, 3,
  	-1, -1, -1, -1, -1, -1 } ;
---- lighter-1.1.2.orig/KmerCode.h
-+++ lighter-1.1.2/KmerCode.h
+--- lighter.orig/KmerCode.h
++++ lighter/KmerCode.h
 @@ -4,7 +4,7 @@
  #include <stdio.h>
  #include "utils.h"
@@ -33,8 +33,8 @@ Description: lighter fails to build from source, because:
  extern char numToNuc[26] ;
  
  const int K_BLOCK_NUM = ( MAX_KMER_LENGTH - 1 ) / ( sizeof( uint64_t ) * 4 ) + 1 ;
---- lighter-1.1.2.orig/ErrorCorrection.cpp
-+++ lighter-1.1.2/ErrorCorrection.cpp
+--- lighter.orig/ErrorCorrection.cpp
++++ lighter/ErrorCorrection.cpp
 @@ -3,7 +3,7 @@
  
  //#define DEBUG 


=====================================
main.cpp
=====================================
@@ -18,7 +18,7 @@
 #include "pthread.h"
 
 
-char LIGHTER_VERSION[] = "Lighter v1.1.2" ;
+char LIGHTER_VERSION[] = "Lighter v1.1.3" ;
 
 char nucToNum[26] = { 0, -1, 1, -1, -1, -1, 2, 
 	-1, -1, -1, -1, -1, -1, -1,
@@ -375,6 +375,16 @@ int main( int argc, char *argv[] )
 		}
 		else if ( !strcmp( "-od", argv[i] ) )
 		{
+			int j ;
+			for (j = 0 ; argv[i + 1][j] ; ++j)
+			{
+				if (argv[i + 1][j] == '/')
+				{
+					argv[i + 1][j] = '\0' ;
+					mkdir( argv[i + 1], 0700 ) ;
+					argv[i + 1][j] = '/' ;
+				}
+			}
 			mkdir( argv[i + 1], 0700 ) ;
 			reads.SetOutputDirectory( argv[i + 1] ) ;
 			++i ;



View it on GitLab: https://salsa.debian.org/med-team/lighter/-/compare/1987ec6b2caf26262955822fa2e68d28a5324523...f1302a489250637ece0f4fcc2701ce16b2fb0c36

-- 
View it on GitLab: https://salsa.debian.org/med-team/lighter/-/compare/1987ec6b2caf26262955822fa2e68d28a5324523...f1302a489250637ece0f4fcc2701ce16b2fb0c36
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