debian/changelog

+libssw (1.1-2) unstable; urgency=medium
+
+  * Team upload.
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.5
+  * d/rules:
+     - Respect DEB_BUILD_OPTIONS in override_dh_auto_test
+     - Do not parse d/changelog
+
+ -- Andreas Tille <tille@debian.org>  Mon, 16 Jul 2018 10:11:08 +0200
+
 libssw (1.1-1) unstable; urgency=medium
 
   [ Sascha Steinbiss ]

debian/compat

-9
+11

debian/control

 Source: libssw
-Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Sascha Steinbiss <satta@debian.org>
-Build-Depends: debhelper (>= 9.20151004),
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~),
                default-jdk-headless,
                javahelper,
-               dh-autoreconf,
                help2man,
                zlib1g-dev,
                maven-repo-helper
-Standards-Version: 3.9.8
-Testsuite: autopkgtest
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libssw.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/libssw.git
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/libssw
+Vcs-Git: https://salsa.debian.org/med-team/libssw.git
 Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
 
 Package: libssw0
@@ -36,7 +34,6 @@ Description: fast SIMD parallelized implementation of the Smith-Waterman algorit
  the sub-optimal alignment score and location heuristically.
 
 Package: libssw-dev
-Provides: libssw-dev
 Architecture: any-amd64 x32
 Multi-Arch: same
 Section: libdevel
@@ -44,6 +41,7 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          libssw0 (= ${binary:Version})
 Pre-Depends: ${misc:Pre-Depends}
+Provides: libssw-dev
 Description: Development headers and static libraries for libssw
  This package provides development headers and static libraries for libssw,
  a fast implementation of the Smith-Waterman algorithm using

debian/patches/gcc_fix.patch

-Description: fix building with GCC 5
- Apparently binaries built with GCC 5 (and 6) will create a
- binary that yields wrong alignments. While recording alignment
- backtraces as edit operations, almost all indels get recorded as
- replacements, which corrupts the output.
- This has been reported upstream; this fix makes GCC build properly
- behaving binaries, possibly at some performance expense as it
- involves reducing the optimization level and removing inlining hints.
-Author: Sascha Steinbiss <satta@debian.org>
-Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/issues/37
-Last-Update: 2016-07-19 
---- a/src/ssw.c
-+++ b/src/ssw.c
-@@ -529,6 +529,37 @@
- 	return bests;
- }
- 
-+/*!     @function               Produce CIGAR 32-bit unsigned integer from CIGAR operation and CIGAR length
-+        @param  length          length of CIGAR
-+        @param  op_letter       CIGAR operation character ('M', 'I', etc)
-+        @return                 32-bit unsigned integer, representing encoded CIGAR operation and length
-+*/
-+uint32_t to_cigar_int (uint32_t length, char op_letter)
-+{
-+        switch (op_letter) {
-+                case 'M': /* alignment match (can be a sequence match or mismatch */
-+                default:
-+                        return length << BAM_CIGAR_SHIFT;
-+                case 'S': /* soft clipping (clipped sequences present in SEQ) */
-+                        return (length << BAM_CIGAR_SHIFT) | (4u);
-+                case 'D': /* deletion from the reference */
-+                        return (length << BAM_CIGAR_SHIFT) | (2u);
-+                case 'I': /* insertion to the reference */
-+                        return (length << BAM_CIGAR_SHIFT) | (1u);
-+                case 'H': /* hard clipping (clipped sequences NOT present in SEQ) */
-+                        return (length << BAM_CIGAR_SHIFT) | (5u);
-+                case 'N': /* skipped region from the reference */
-+                        return (length << BAM_CIGAR_SHIFT) | (3u);
-+                case 'P': /* padding (silent deletion from padded reference) */
-+                        return (length << BAM_CIGAR_SHIFT) | (6u);
-+                case '=': /* sequence match */
-+                        return (length << BAM_CIGAR_SHIFT) | (7u);
-+                case 'X': /* sequence mismatch */
-+                        return (length << BAM_CIGAR_SHIFT) | (8u);
-+        }
-+        return (uint32_t)-1; // This never happens
-+}
-+
- static cigar* banded_sw (const int8_t* ref,
- 				 const int8_t* read,
- 				 int32_t refLen,
---- a/src/ssw.h
-+++ b/src/ssw.h
-@@ -22,7 +22,7 @@
- 
- #define MAPSTR "MIDNSHP=X"
- #ifndef BAM_CIGAR_SHIFT
--#define BAM_CIGAR_SHIFT 4
-+#define BAM_CIGAR_SHIFT 4u
- #endif
- 
- 
-@@ -134,32 +134,7 @@
- 	@param	op_letter	CIGAR operation character ('M', 'I', etc)
- 	@return			32-bit unsigned integer, representing encoded CIGAR operation and length
- */
--static inline uint32_t to_cigar_int (uint32_t length, char op_letter)
--{
--	switch (op_letter) {
--		case 'M': /* alignment match (can be a sequence match or mismatch */
--		default:
--			return length << BAM_CIGAR_SHIFT;
--		case 'S': /* soft clipping (clipped sequences present in SEQ) */
--			return (length << BAM_CIGAR_SHIFT) | (4u);
--		case 'D': /* deletion from the reference */
--			return (length << BAM_CIGAR_SHIFT) | (2u);
--		case 'I': /* insertion to the reference */
--			return (length << BAM_CIGAR_SHIFT) | (1u);
--		case 'H': /* hard clipping (clipped sequences NOT present in SEQ) */
--			return (length << BAM_CIGAR_SHIFT) | (5u);
--		case 'N': /* skipped region from the reference */
--			return (length << BAM_CIGAR_SHIFT) | (3u);
--		case 'P': /* padding (silent deletion from padded reference) */
--			return (length << BAM_CIGAR_SHIFT) | (6u);
--		case '=': /* sequence match */
--			return (length << BAM_CIGAR_SHIFT) | (7u);
--		case 'X': /* sequence mismatch */
--			return (length << BAM_CIGAR_SHIFT) | (8u);
--	}
--	return (uint32_t)-1; // This never happens
--}
--
-+uint32_t to_cigar_int (uint32_t length, char op_letter);
- 
- /*!	@function		Extract CIGAR operation character from CIGAR 32-bit unsigned integer
- 	@param	cigar_int	32-bit unsigned integer, representing encoded CIGAR operation and length

debian/rules

@@ -2,8 +2,8 @@
 
 # DH_VERBOSE := 1
 export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
-DEBVERS := $(shell dpkg-parsechangelog | sed -n -e 's/^Version: //p')
-PKG_VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/-.*//')
+
+include /usr/share/dpkg/default.mk
 
 %:
 	dh $@ --with javahelper --with jh_maven_repo_helper
@@ -16,7 +16,7 @@ override_dh_auto_build:
 	$(MAKE) -C src default java
 
 override_dh_auto_install: debian/libssw0.install debian/libssw-dev.install debian/libssw-dev.links debian/libssw-java.install debian/libssw-java.links
-	mv src/ssw.jar src/ssw-$(PKG_VERSION).jar
+	mv src/ssw.jar src/ssw-$(DEB_VERSION_UPSTREAM).jar
 	dh_auto_install
 
 override_dh_installman:
@@ -28,12 +28,14 @@ override_dh_installman:
 	dh_installman
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	src/example_c
 	src/example_cpp
+endif
 
 debian/%.install: debian/%.install.in
 	sed 's/@DEB_HOST_MULTIARCH@/$(DEB_HOST_MULTIARCH)/g' $< > $@
 
 debian/%.links: debian/%.links.in
 	sed -e 's/@DEB_HOST_MULTIARCH@/$(DEB_HOST_MULTIARCH)/g' \
-            -e 's/@DEB_JAVA_PKG_VERSION@/$(PKG_VERSION)/g' $< > $@
+            -e 's/@DEB_JAVA_PKG_VERSION@/$(DEB_VERSION_UPSTREAM)/g' $< > $@