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 <[email protected]>
--- 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 <[email protected]>
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 <[email protected]>
--- 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 <[email protected]>
#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
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