[med-svn] [Git][med-team/subread][master] Refresh patches

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / subread


Commits:
80c6355b by Nilesh Patra at 2021-05-19T22:22:51+05:30
Refresh patches

- - - - -


3 changed files:

- debian/patches/2to3.patch
- debian/patches/arch_specific_flags.patch
- debian/patches/fix_ftbfs_kfreebsd.patch


Changes:

=====================================
debian/patches/2to3.patch
=====================================
@@ -5,7 +5,7 @@ Last-Update: Thu, 05 Sep 2019 09:01:45 +0200
 
 --- a/test/subread-align/readname_cigar_match.py
 +++ b/test/subread-align/readname_cigar_match.py
-@@ -68,10 +68,10 @@ while True:
+@@ -68,10 +68,10 @@
  
  	if not is_correct:
  		if is_cigar_problem:
@@ -21,7 +21,7 @@ Last-Update: Thu, 05 Sep 2019 09:01:45 +0200
 +print("RES: %d reads\t%d unmapped\t%d error_pos\t%d error_cigar\t%d correct_indel"%(all_r,unmapped, error_pos, error_cig, correct_indel))
 --- a/test/subread-align/readname_ora_match.py
 +++ b/test/subread-align/readname_ora_match.py
-@@ -29,7 +29,7 @@ def main():
+@@ -29,7 +29,7 @@
  		line +=1
  
  		if line % 100000 == 0:
@@ -30,7 +30,7 @@ Last-Update: Thu, 05 Sep 2019 09:01:45 +0200
  
  		if fl.find("NNNNNNNN")>0:
  			NN+=1
-@@ -76,8 +76,8 @@ def main():
+@@ -76,8 +76,8 @@
  
  		old_read_name = t_name
  


=====================================
debian/patches/arch_specific_flags.patch
=====================================
@@ -9,7 +9,7 @@ Description: Inject architecture specific flags:
 Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
 --- a/src/Makefile.Linux
 +++ b/src/Makefile.Linux
-@@ -7,9 +7,9 @@ OPT_LEVEL = 3
+@@ -7,9 +7,9 @@
  include makefile.version
  -include ~/.R/DBPZ_debug_makefile
  
@@ -24,7 +24,7 @@ Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
  ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib input-blc
 --- a/src/longread-one/Makefile
 +++ b/src/longread-one/Makefile
-@@ -4,9 +4,9 @@ OPT_LEVEL = 3
+@@ -4,9 +4,9 @@
  include ../makefile.version
  include make.version
  


=====================================
debian/patches/fix_ftbfs_kfreebsd.patch
=====================================
@@ -2,7 +2,7 @@ Subject: Fix ftbfs on kfreebsd
 From: Alex Mestiashvili <alex at biotec.tu-dresden.de>
 --- a/src/HelperFunctions.c
 +++ b/src/HelperFunctions.c
-@@ -848,6 +848,9 @@ int mac_str(char * str_buff)
+@@ -849,6 +849,9 @@
  #if defined(FREEBSD) || defined(__MINGW32__)
  	return 1;
  #else
@@ -12,7 +12,7 @@ From: Alex Mestiashvili <alex at biotec.tu-dresden.de>
  #ifdef MACOS
      int         mib[6], x1, ret = 1;
  	size_t		len;
-@@ -940,6 +943,7 @@ int mac_str(char * str_buff)
+@@ -941,6 +944,7 @@
  	return 1;
  #endif
  #endif



View it on GitLab: https://salsa.debian.org/med-team/subread/-/commit/80c6355b322521e4765d1668bf2b32ec4fbec1b3

-- 
View it on GitLab: https://salsa.debian.org/med-team/subread/-/commit/80c6355b322521e4765d1668bf2b32ec4fbec1b3
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210519/e490b5fd/attachment-0001.htm>