[med-svn] [Git][med-team/libssw][master] 8 commits: debhelper 11
Andreas Tille
gitlab at salsa.debian.org
Mon Jul 16 09:17:13 BST 2018
Andreas Tille pushed to branch master at Debian Med / libssw
Commits:
95506176 by Andreas Tille at 2018-07-16T09:59:56+02:00
debhelper 11
- - - - -
3a996008 by Andreas Tille at 2018-07-16T10:02:25+02:00
Point Vcs fields to salsa.debian.org
- - - - -
f07a9e7e by Andreas Tille at 2018-07-16T10:02:25+02:00
Standards-Version: 4.1.5
- - - - -
218faf57 by Andreas Tille at 2018-07-16T10:05:53+02:00
Drop deactivated patch
- - - - -
e018da4e by Andreas Tille at 2018-07-16T10:06:15+02:00
Do not mention Testsuite: autopkgtest explicitly
- - - - -
c2460a82 by Andreas Tille at 2018-07-16T10:07:52+02:00
Respect DEB_BUILD_OPTIONS in override_dh_auto_test
- - - - -
89a75d1a by Andreas Tille at 2018-07-16T10:10:56+02:00
Do not parse d/changelog
- - - - -
6aa39fdd by Andreas Tille at 2018-07-16T10:13:15+02:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/compat
- debian/control
- − debian/patches/gcc_fix.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,15 @@
+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 at debian.org> Mon, 16 Jul 2018 10:11:08 +0200
+
libssw (1.1-1) unstable; urgency=medium
[ Sascha Steinbiss ]
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -1,19 +1,17 @@
Source: libssw
-Section: science
-Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <satta at 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 deleted
=====================================
--- a/debian/patches/gcc_fix.patch
+++ /dev/null
@@ -1,96 +0,0 @@
-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 at 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
=====================================
--- a/debian/rules
+++ b/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' $< > $@
View it on GitLab: https://salsa.debian.org/med-team/libssw/compare/9dedb78d6bedecd70f82933ecf32f3b37f9c5afa...6aa39fdd8bd94279a743f6b8f41d756230f0227c
--
View it on GitLab: https://salsa.debian.org/med-team/libssw/compare/9dedb78d6bedecd70f82933ecf32f3b37f9c5afa...6aa39fdd8bd94279a743f6b8f41d756230f0227c
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