[med-svn] [subread] 03/04: d/patches: updated and renamed getopt4exactSNP.patch to getopt.patch fixing 2 more issues with wrong assignment for the getopt_long function

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository subread.

commit 61832cc6f1369d16e6109c3f099e661d7ea28e7c
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon May 18 17:34:30 2015 +0200

    d/patches: updated and renamed getopt4exactSNP.patch to getopt.patch
     fixing 2 more issues with wrong assignment for the getopt_long function
---
 debian/patches/getopt.patch          | 36 ++++++++++++++++++++++++++++++++++++
 debian/patches/getopt4exactSNP.patch | 13 -------------
 debian/patches/series                |  2 +-
 3 files changed, 37 insertions(+), 14 deletions(-)

diff --git a/debian/patches/getopt.patch b/debian/patches/getopt.patch
new file mode 100644
index 0000000..68fdf45
--- /dev/null
+++ b/debian/patches/getopt.patch
@@ -0,0 +1,36 @@
+Description: getopt_long returns int
+Origin: Bug#784929
+--- subread.orig/src/SNPCalling.c
++++ subread/src/SNPCalling.c
+@@ -1524,7 +1524,7 @@
+ 	for(xk1=0;xk1<1;xk1++){
+ 
+ 
+-	char c;
++	int c;
+ 	char in_SAM_file[5000];
+ 	char out_BED_file[300];
+ 	char temp_path[300];
+--- subread.orig/src/removeDupReads.c
++++ subread/src/removeDupReads.c
+@@ -231,7 +231,7 @@
+ int main_repeated_test(int argc,char ** argv)
+ #endif
+ {
+-	char c;
++	int c;
+ 	char input_SAM_file[300];
+ 	char output_SAM_file[300];
+ 	char temp_path[300];
+--- subread.orig/src/index-builder.c
++++ subread/src/index-builder.c
+@@ -977,7 +977,8 @@
+ {
+ 	int threshold = 24, optindex=0;
+ 	int memory_limit;	// 8000 MBytes
+-	char output_file[300], c, tmp_fa_file[300], log_file_name[300];
++	int c;
++	char output_file[300], tmp_fa_file[300], log_file_name[300];
+ 	char *ptr_tmp_fa_file[1];
+ 	unsigned int * chromosome_lengths;
+ 
diff --git a/debian/patches/getopt4exactSNP.patch b/debian/patches/getopt4exactSNP.patch
deleted file mode 100644
index f104e33..0000000
--- a/debian/patches/getopt4exactSNP.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Description: getopt_long return int, not char
-Origin: Bug#784929
---- subread.orig/src/SNPCalling.c
-+++ subread/src/SNPCalling.c
-@@ -1524,7 +1524,7 @@
- 	for(xk1=0;xk1<1;xk1++){
- 
- 
--	char c;
-+	int c;
- 	char in_SAM_file[5000];
- 	char out_BED_file[300];
- 	char temp_path[300];
diff --git a/debian/patches/series b/debian/patches/series
index bd566ca..6c1fbc2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,3 @@
-getopt4exactSNP.patch
+getopt.patch
 gcc_flags_cleanup.patch
 fix_syntax.patch

-- 
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