[med-svn] [Git][med-team/hisat2][master] 3 commits: debian/patches/riscv5: fix compilation on riscv5

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / hisat2


Commits:
4ef97c9b by Michael R. Crusoe at 2021-01-27T16:55:24+01:00
debian/patches/riscv5: fix compilation on riscv5

- - - - -
b3a001b6 by Michael R. Crusoe at 2021-01-27T17:34:03+01:00
routine-update: Standards-Version: 4.5.1

- - - - -
5c4b14b9 by Michael R. Crusoe at 2021-01-27T17:34:32+01:00
routine-update: Ready to upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/riscv5
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+hisat2 (2.2.1-2) unstable; urgency=medium
+
+  * debian/patches/riscv5: fix compilation on riscv5
+  * Standards-Version: 4.5.1 (routine-update)
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Wed, 27 Jan 2021 17:34:32 +0100
+
 hisat2 (2.2.1-1) unstable; urgency=medium
 
   [ Steffen Moeller ]


=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13),
                help2man <!nodoc>,
                pandoc <!nodoc>,
                python3:any <!nodoc>
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
 Vcs-Browser: https://salsa.debian.org/med-team/hisat2
 Vcs-Git: https://salsa.debian.org/med-team/hisat2.git
 Homepage: https://daehwankimlab.github.io/hisat2/


=====================================
debian/patches/riscv5
=====================================
@@ -0,0 +1,35 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Fix compilation on riscv5
+--- hisat2.orig/alphabet.cpp
++++ hisat2/alphabet.cpp
+@@ -400,7 +400,7 @@
+ 
+ const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn";
+ 
+-char mask2iupac[16] = {
++int mask2iupac[16] = {
+ 	-1,
+ 	'A', // 0001
+ 	'C', // 0010
+--- hisat2.orig/alphabet.h
++++ hisat2/alphabet.h
+@@ -65,7 +65,7 @@
+ /// corresponding 2-bit nucleotide
+ extern uint8_t nuccol2nuc[5][5];
+ /// Convert a 4-bit mask into an IUPAC code
+-extern char mask2iupac[16];
++extern int mask2iupac[16];
+ 
+ /// Convert an ascii color to an ascii dna char
+ extern char col2dna[];
+--- hisat2.orig/sstring.h
++++ hisat2/sstring.h
+@@ -3326,7 +3326,7 @@
+ 	 */
+ 	char toChar(size_t idx) const {
+ 		assert_range((int)this->cs_[idx], 0, 15);
+-		return mask2iupac[(int)this->cs_[idx]];
++		return (char)mask2iupac[(int)this->cs_[idx]];
+ 	}
+ 
+ 	/**


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ compilerflags
 simde
 python3
 fix-manual
+riscv5



View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/compare/ef149b86ac639fd8bafcd909f62ad912a8124e1a...5c4b14b9b0cbab8d6667ac3848219e7942101290

-- 
View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/compare/ef149b86ac639fd8bafcd909f62ad912a8124e1a...5c4b14b9b0cbab8d6667ac3848219e7942101290
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