[med-svn] [Git][med-team/libssw][master] Revert to 64e59f110f2a2a782640b88e2219a3bf3250e5cf after discussing with...
Andreas Tille
gitlab at salsa.debian.org
Sat Apr 11 18:13:00 BST 2020
Andreas Tille pushed to branch master at Debian Med / libssw
Commits:
92aa9391 by Andreas Tille at 2020-04-11T19:11:34+02:00
Revert to 64e59f110f2a2a782640b88e2219a3bf3250e5cf after discussing with Michael Crusoe who considers packaging latest upstream to hard for our reverse dependencies
- - - - -
11 changed files:
- debian/changelog
- debian/control
- + debian/libssw0.install.in
- debian/libssw1.symbols → debian/libssw0.symbols
- − debian/libssw1.install.in
- debian/patches/build_all_libs.patch
- debian/patches/hardening.patch
- debian/patches/rename_tool.patch
- debian/patches/simde.patch
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,12 +1,3 @@
-libssw (1.2.4+git20190312.cabdab1-1) UNRELEASED; urgency=medium
-
- * Team upload.
- * New upstream version
- * d/watch: use Git mode since upstream stopped tagging releases
- * Need to bump soversion since upstream has dropped symbols
-
- -- Andreas Tille <tille at debian.org> Sat, 11 Apr 2020 10:19:51 +0200
-
libssw (1.1-10) UNRELEASED; urgency=medium
* Improve crossbuilding
=====================================
debian/control
=====================================
@@ -16,7 +16,7 @@ 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: libssw1
+Package: libssw0
Architecture: any
Multi-Arch: same
Section: libs
@@ -40,7 +40,7 @@ Architecture: any
Multi-Arch: same
Section: libdevel
Depends: ${misc:Depends},
- libssw1 (= ${binary:Version})
+ libssw0 (= ${binary:Version})
Pre-Depends: ${misc:Pre-Depends}
Provides: libssw-dev
Description: Development headers and static libraries for libssw
@@ -66,7 +66,7 @@ Package: ssw-align
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- libssw1 (= ${binary:Version})
+ libssw0 (= ${binary:Version})
Description: Smith-Waterman aligner based on libssw
This package provides a command-line aligner based on the libssw library,
a fast SIMD accelerated implementation of the Smith-Waterman algorithm.
=====================================
debian/libssw0.install.in
=====================================
@@ -0,0 +1 @@
+src/libssw.so.0 usr/lib/@DEB_HOST_MULTIARCH@/
=====================================
debian/libssw1.symbols → debian/libssw0.symbols
=====================================
@@ -1,4 +1,4 @@
-libssw.so.1 libssw1 #MINVER#
+libssw.so.0 libssw0 #MINVER#
* Build-Depends-Package: libssw-dev
_Z16store_previous_maPjS_PiS0_S_ at Base 1.1
_Z9add_cigarPjPiS0_jc at Base 1.1
@@ -19,16 +19,16 @@ libssw.so.1 libssw1 #MINVER#
_ZN20StripedSmithWaterman7AlignerD1Ev at Base 1.1
_ZN20StripedSmithWaterman7AlignerD2Ev at Base 1.1
_ZNK20StripedSmithWaterman7Aligner13TranslateBaseEPKcRKiPa at Base 1.1
- _ZNK20StripedSmithWaterman7Aligner5AlignEPKcRKNS_6FilterEPNS_9AlignmentEi at Base 1.2.4
- _ZNK20StripedSmithWaterman7Aligner5AlignEPKcS2_RKiRKNS_6FilterEPNS_9AlignmentEi at Base 1.2.4
+ _ZNK20StripedSmithWaterman7Aligner5AlignEPKcRKNS_6FilterEPNS_9AlignmentE at Base 1.1
+ _ZNK20StripedSmithWaterman7Aligner5AlignEPKcS2_RKiRKNS_6FilterEPNS_9AlignmentE at Base 1.1
_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 1.1
_ZNSt6vectorIjSaIjEEaSERKS1_ at Base 1.1
_ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 1.1
_ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 1.1
_ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 1.1
align_destroy at Base 1.1
- encoded_ops at Base 1.2.4
init_destroy at Base 1.1
mark_mismatch at Base 1.1
ssw_align at Base 1.1
ssw_init at Base 1.1
+ to_cigar_int at Base 1.1
=====================================
debian/libssw1.install.in deleted
=====================================
@@ -1 +0,0 @@
-src/libssw.so.1 usr/lib/@DEB_HOST_MULTIARCH@/
=====================================
debian/patches/build_all_libs.patch
=====================================
@@ -6,12 +6,12 @@ Description: build all libraries
Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/src/Makefile
+++ b/src/Makefile
-@@ -5,26 +5,32 @@ CXXFLAGS := $(CFLAGS)
+@@ -5,24 +5,29 @@
LOBJS = ssw.o
LCPPOBJS = ssw_cpp.o
PROG = ssw_test
-LIB = libssw.so
-+SOVERS=.1
++SOVERS=.0
+LIB = libssw.so$(SOVERS)
+STATICLIB = libssw.a
EXAMPLE = example_c
@@ -25,8 +25,6 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
.PHONY: all default java clean
- core: $(PROG)
-
-default: $(PROG) $(EXAMPLE) $(EXAMPLE_CPP) $(LIB)
+default: $(PROG) $(EXAMPLE) $(EXAMPLE_CPP) $(LIB) $(STATICLIB)
@@ -39,13 +37,12 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
+$(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^
+
-+
+$(STATICLIB): $(LOBJS) $(LCPPOBJS)
-+ $(AR) rcs $@ $^
++ ar rcs $@ $^
$(PROG): main.c kseq.h
-@@ -40,10 +46,10 @@ $(JAVA_LIB): sswjni.c ssw.c ssw.h
+@@ -38,10 +43,10 @@
$(CC) $(CFLAGS) $(JAVA_INLCUDES) -fPIC -shared -rdynamic -o $@ $< ssw.c
$(JAVA_JAR): $(JAVA_OBJ)
@@ -58,7 +55,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
ssw.o: ssw.c ssw.h
$(CC) -c -o $@ $< $(CFLAGS)
-@@ -52,4 +58,4 @@ ssw_cpp.o: ssw_cpp.cpp ssw_cpp.h ssw.h
+@@ -50,4 +55,4 @@
$(CXX) -c -o $@ $< $(CXXFLAGS)
clean:
=====================================
debian/patches/hardening.patch
=====================================
@@ -1,7 +1,7 @@
Description: add hardening
Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/src/Makefile
-+++ b/src/Makefile
+--- libssw.orig/src/Makefile
++++ libssw/src/Makefile
@@ -1,7 +1,8 @@
-CC = gcc
-CXX = g++
@@ -15,16 +15,19 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
LOBJS = ssw.o
LCPPOBJS = ssw_cpp.o
PROG = ssw_test
-@@ -26,7 +27,7 @@ all: default java
+@@ -24,23 +25,23 @@
java: $(JAVA_JAR) $(JAVA_LIB)
$(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^ $(LDFLAGS)
-
$(STATICLIB): $(LOBJS) $(LCPPOBJS)
-@@ -37,13 +38,13 @@ $(PROG): main.c kseq.h
+- ar rcs $@ $^
++ $(AR) rcs $@ $^
+
+ $(PROG): main.c kseq.h
+
$(EXAMPLE): example.c
$(PROG) $(EXAMPLE): $(LOBJS)
@@ -41,7 +44,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
$(JAVA_JAR): $(JAVA_OBJ)
jar cvf $@ $^
-@@ -52,10 +53,10 @@ $(JAVA_JAR): $(JAVA_OBJ)
+@@ -49,10 +50,10 @@
javac -target 1.6 -source 1.6 $<
ssw.o: ssw.c ssw.h
=====================================
debian/patches/rename_tool.patch
=====================================
@@ -2,24 +2,24 @@ Description: build command line aligner
This patch ensures that 'ssw_test' is called 'ssw-align' in Debian
and also links against libssw.
Author: Sascha Steinbiss <satta at debian.org>
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -5,9 +5,10 @@ AR ?= ar
+--- libssw.orig/src/Makefile
++++ libssw/src/Makefile
+@@ -5,9 +5,10 @@
#CXXFLAGS := $(CFLAGS)
LOBJS = ssw.o
LCPPOBJS = ssw_cpp.o
-PROG = ssw_test
+PROG = ssw-align
- SOVERS=.1
+ SOVERS=.0
LIB = libssw.so$(SOVERS)
+LLIB = libssw.so
STATICLIB = libssw.a
EXAMPLE = example_c
EXAMPLE_CPP = example_cpp
-@@ -30,14 +31,18 @@ $(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cp
+@@ -27,14 +28,18 @@
+ $(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp
$(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^ $(LDFLAGS)
-
+$(LLIB): $(LIB)
+ ln -s $< $@
+
@@ -37,9 +37,9 @@ Author: Sascha Steinbiss <satta at debian.org>
$(CC) -o $@ $(filter-out %.h,$^) $(CPPFLAGS) $(CFLAGS) -lm -lz $(LDFLAGS)
$(EXAMPLE_CPP): example.cpp $(LOBJS) $(LCPPOBJS)
---- a/src/main.c
-+++ b/src/main.c
-@@ -271,7 +271,7 @@ int main (int argc, char * const argv[])
+--- libssw.orig/src/main.c
++++ libssw/src/main.c
+@@ -297,7 +297,7 @@
}
if (optind + 2 > argc) {
fprintf(stderr, "\n");
=====================================
debian/patches/simde.patch
=====================================
@@ -1,18 +1,18 @@
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: use the simde header library for greater compatibility
Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pull/69
---- a/src/ssw.c
-+++ b/src/ssw.c
-@@ -67,7 +67,7 @@
+--- libssw.orig/src/ssw.c
++++ libssw/src/ssw.c
+@@ -35,7 +35,7 @@
+ *
*/
- //#include <nmmintrin.h>
-#include <emmintrin.h>
+#include "../debian/include/simde/x86/sse2.h"
#include <stdint.h>
#include <stdlib.h>
#include <stdio.h>
-@@ -108,8 +108,8 @@ typedef struct {
+@@ -76,8 +76,8 @@
} cigar;
struct _profile{
@@ -23,7 +23,7 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
const int8_t* read;
const int8_t* mat;
int32_t readLen;
-@@ -155,7 +155,7 @@ const uint8_t encoded_ops[] = {
+@@ -86,7 +86,7 @@
};
/* Generate query profile rearrange query sequence & calculate the weight of match/mismatch. */
@@ -32,7 +32,7 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
const int8_t* mat,
const int32_t readLen,
const int32_t n, /* the edge length of the squre matrix mat */
-@@ -165,7 +165,7 @@ static __m128i* qP_byte (const int8_t* r
+@@ -96,7 +96,7 @@
Each piece is 8 bit. Split the read into 16 segments.
Calculat 16 segments in parallel.
*/
@@ -41,7 +41,7 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
int8_t* t = (int8_t*)vProfile;
int32_t nt, i, j, segNum;
-@@ -195,7 +195,7 @@ static alignment_end* sw_sse2_byte (cons
+@@ -126,7 +126,7 @@
int32_t readLen,
const uint8_t weight_gapO, /* will be used as - */
const uint8_t weight_gapE, /* will be used as - */
@@ -50,24 +50,24 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
uint8_t terminate, /* the best alignment score: used to terminate
the matrix calculation when locating the
alignment beginning point. If this score
-@@ -204,11 +204,11 @@ static alignment_end* sw_sse2_byte (cons
+@@ -134,11 +134,11 @@
+ uint8_t bias, /* Shift 0 point to a positive value. */
int32_t maskLen) {
- // Put the largest number of the 16 numbers in vm into m.
-#define max16(m, vm) (vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 8)); \
- (vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 4)); \
- (vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 2)); \
- (vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 1)); \
- (m) = _mm_extract_epi16((vm), 0)
+#define max16(m, vm) (vm) = simde_mm_max_epu8((vm), simde_mm_srli_si128((vm), 8)); \
-+ (vm) = simde_mm_max_epu8((vm), simde_mm_srli_si128((vm), 4)); \
-+ (vm) = simde_mm_max_epu8((vm), simde_mm_srli_si128((vm), 2)); \
-+ (vm) = simde_mm_max_epu8((vm), simde_mm_srli_si128((vm), 1)); \
-+ (m) = simde_mm_extract_epi16((vm), 0)
++ (vm) = simde_mm_max_epu8((vm), simde_mm_srli_si128((vm), 4)); \
++ (vm) = simde_mm_max_epu8((vm), simde_mm_srli_si128((vm), 2)); \
++ (vm) = simde_mm_max_epu8((vm), simde_mm_srli_si128((vm), 1)); \
++ (m) = simde_mm_extract_epi16((vm), 0)
uint8_t max = 0; /* the max alignment score */
int32_t end_read = readLen - 1;
-@@ -222,26 +222,26 @@ static alignment_end* sw_sse2_byte (cons
+@@ -152,26 +152,26 @@
int32_t* end_read_column = (int32_t*) calloc(refLen, sizeof(int32_t));
/* Define 16 byte 0 vector. */
@@ -83,7 +83,7 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
+ simde__m128i* pvE = (simde__m128i*) calloc(segLen, sizeof(simde__m128i));
+ simde__m128i* pvHmax = (simde__m128i*) calloc(segLen, sizeof(simde__m128i));
- int32_t i, j, k;
+ int32_t i, j;
/* 16 byte insertion begin vector */
- __m128i vGapO = _mm_set1_epi8(weight_gapO);
+ simde__m128i vGapO = simde_mm_set1_epi8(weight_gapO);
@@ -105,7 +105,7 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
int32_t edge, begin = 0, end = refLen, step = 1;
/* outer loop to process the reference sequence */
-@@ -252,66 +252,66 @@ static alignment_end* sw_sse2_byte (cons
+@@ -182,84 +182,84 @@
}
for (i = begin; LIKELY(i != end); i += step) {
int32_t cmp;
@@ -169,29 +169,55 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
+ vH = simde_mm_load_si128(pvHLoad + j);
}
- /* Lazy_F loop: has been revised to disallow adjecent insertion and then deletion, so don't update E(i, j), learn from SWPS3 */
- for (k = 0; LIKELY(k < 16); ++k) {
-- vF = _mm_slli_si128 (vF, 1);
-+ vF = simde_mm_slli_si128 (vF, 1);
- for (j = 0; LIKELY(j < segLen); ++j) {
-- vH = _mm_load_si128(pvHStore + j);
-- vH = _mm_max_epu8(vH, vF);
-- vMaxColumn = _mm_max_epu8(vMaxColumn, vH); // newly added line
-- _mm_store_si128(pvHStore + j, vH);
-- vH = _mm_subs_epu8(vH, vGapO);
-- vF = _mm_subs_epu8(vF, vGapE);
-- if (UNLIKELY(! _mm_movemask_epi8(_mm_cmpgt_epi8(vF, vH)))) goto end;
-+ vH = simde_mm_load_si128(pvHStore + j);
-+ vH = simde_mm_max_epu8(vH, vF);
-+ vMaxColumn = simde_mm_max_epu8(vMaxColumn, vH); // newly added line
-+ simde_mm_store_si128(pvHStore + j, vH);
-+ vH = simde_mm_subs_epu8(vH, vGapO);
-+ vF = simde_mm_subs_epu8(vF, vGapE);
-+ if (UNLIKELY(! simde_mm_movemask_epi8(simde_mm_cmpgt_epi8(vF, vH)))) goto end;
- }
- }
-
- end:
+ /* Lazy_F loop: has been revised to disallow adjecent insertion and then deletion, so don't update E(i, j), learn from SWPS3 */
+ /* reset pointers to the start of the saved data */
+ j = 0;
+- vH = _mm_load_si128 (pvHStore + j);
++ vH = simde_mm_load_si128 (pvHStore + j);
+
+ /* the computed vF value is for the given column. since */
+ /* we are at the end, we need to shift the vF value over */
+ /* to the next column. */
+- vF = _mm_slli_si128 (vF, 1);
+- vTemp = _mm_subs_epu8 (vH, vGapO);
+- vTemp = _mm_subs_epu8 (vF, vTemp);
+- vTemp = _mm_cmpeq_epi8 (vTemp, vZero);
+- cmp = _mm_movemask_epi8 (vTemp);
++ vF = simde_mm_slli_si128 (vF, 1);
++ vTemp = simde_mm_subs_epu8 (vH, vGapO);
++ vTemp = simde_mm_subs_epu8 (vF, vTemp);
++ vTemp = simde_mm_cmpeq_epi8 (vTemp, vZero);
++ cmp = simde_mm_movemask_epi8 (vTemp);
+
+ while (cmp != 0xffff)
+ {
+- vH = _mm_max_epu8 (vH, vF);
+- vMaxColumn = _mm_max_epu8(vMaxColumn, vH);
+- _mm_store_si128 (pvHStore + j, vH);
+- vF = _mm_subs_epu8 (vF, vGapE);
++ vH = simde_mm_max_epu8 (vH, vF);
++ vMaxColumn = simde_mm_max_epu8(vMaxColumn, vH);
++ simde_mm_store_si128 (pvHStore + j, vH);
++ vF = simde_mm_subs_epu8 (vF, vGapE);
+ j++;
+ if (j >= segLen)
+ {
+ j = 0;
+- vF = _mm_slli_si128 (vF, 1);
++ vF = simde_mm_slli_si128 (vF, 1);
+ }
+- vH = _mm_load_si128 (pvHStore + j);
++ vH = simde_mm_load_si128 (pvHStore + j);
+
+- vTemp = _mm_subs_epu8 (vH, vGapO);
+- vTemp = _mm_subs_epu8 (vF, vTemp);
+- vTemp = _mm_cmpeq_epi8 (vTemp, vZero);
+- cmp = _mm_movemask_epi8 (vTemp);
++ vTemp = simde_mm_subs_epu8 (vH, vGapO);
++ vTemp = simde_mm_subs_epu8 (vF, vTemp);
++ vTemp = simde_mm_cmpeq_epi8 (vTemp, vZero);
++ cmp = simde_mm_movemask_epi8 (vTemp);
+ }
- vMaxScore = _mm_max_epu8(vMaxScore, vMaxColumn);
- vTemp = _mm_cmpeq_epi8(vMaxMark, vMaxScore);
@@ -202,7 +228,7 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
if (cmp != 0xffff) {
uint8_t temp;
vMaxMark = vMaxScore;
-@@ -379,13 +379,13 @@ end:
+@@ -327,13 +327,13 @@
return bests;
}
@@ -218,7 +244,7 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
int16_t* t = (int16_t*)vProfile;
int32_t nt, i, j;
int32_t segNum;
-@@ -409,14 +409,14 @@ static alignment_end* sw_sse2_word (cons
+@@ -357,14 +357,14 @@
int32_t readLen,
const uint8_t weight_gapO, /* will be used as - */
const uint8_t weight_gapE, /* will be used as - */
@@ -238,7 +264,7 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
uint16_t max = 0; /* the max alignment score */
int32_t end_read = readLen - 1;
-@@ -430,23 +430,23 @@ static alignment_end* sw_sse2_word (cons
+@@ -378,23 +378,23 @@
int32_t* end_read_column = (int32_t*) calloc(refLen, sizeof(int32_t));
/* Define 16 byte 0 vector. */
@@ -272,7 +298,7 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
int32_t edge, begin = 0, end = refLen, step = 1;
/* outer loop to process the reference sequence */
-@@ -457,66 +457,66 @@ static alignment_end* sw_sse2_word (cons
+@@ -405,66 +405,66 @@
}
for (i = begin; LIKELY(i != end); i += step) {
int32_t cmp;
@@ -369,7 +395,7 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
if (cmp != 0xffff) {
uint16_t temp;
vMaxMark = vMaxScore;
-@@ -822,7 +822,7 @@ s_align* ssw_align (const s_profile* pro
+@@ -801,7 +801,7 @@
const int32_t maskLen) {
alignment_end* bests = 0, *bests_reverse = 0;
@@ -378,8 +404,8 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
int32_t word = 0, band_width = 0, readLen = prof->readLen;
int8_t* read_reverse = 0;
cigar* path;
---- a/src/ssw.h
-+++ b/src/ssw.h
+--- libssw.orig/src/ssw.h
++++ libssw/src/ssw.h
@@ -14,7 +14,6 @@
#include <stdio.h>
#include <stdint.h>
@@ -388,8 +414,8 @@ Forwarded: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pu
#ifdef __cplusplus
extern "C" {
---- a/src/main.c
-+++ b/src/main.c
+--- libssw.orig/src/main.c
++++ libssw/src/main.c
@@ -6,7 +6,6 @@
#include <stdlib.h>
=====================================
debian/rules
=====================================
@@ -22,7 +22,7 @@ override_dh_auto_clean:
override_dh_auto_build:
$(MAKE) -C src default java
-override_dh_auto_install: debian/libssw1.install debian/libssw-dev.install debian/libssw-dev.links debian/libssw-java.install debian/libssw-java.links
+override_dh_auto_install: debian/libssw0.install debian/libssw-dev.install debian/libssw-dev.links debian/libssw-java.install debian/libssw-java.links
mv src/ssw.jar src/ssw-$(DEB_VERSION_UPSTREAM).jar
dh_auto_install
=====================================
debian/watch
=====================================
@@ -1,9 +1,2 @@
-version=4
-
-opts="mode=git,pretty=1.2.4+git%cd.%h" \
- https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library.git HEAD
-
-
-# https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/tags .*/v?(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
-# Asked for tagging releases:
-# https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/issues/72
+version=3
+https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/tags .*/v?(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
View it on GitLab: https://salsa.debian.org/med-team/libssw/-/commit/92aa9391fd98483ffd8e367613e61845399cc79e
--
View it on GitLab: https://salsa.debian.org/med-team/libssw/-/commit/92aa9391fd98483ffd8e367613e61845399cc79e
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