[med-svn] [Git][med-team/last-align][master] Refresh patches before routine update
Charles Plessy (@plessy)
gitlab at salsa.debian.org
Mon Dec 18 02:42:17 GMT 2023
Charles Plessy pushed to branch master at Debian Med / last-align
Commits:
a09af6b6 by Charles Plessy at 2023-12-18T02:41:42+00:00
Refresh patches before routine update
- - - - -
2 changed files:
- debian/patches/helpMakefiles.patch
- debian/patches/simde
Changes:
=====================================
debian/patches/helpMakefiles.patch
=====================================
@@ -23,52 +23,20 @@ Description: Propagate variables to Makefile
alpObj = alp/sls_alignment_evaluer.o alp/sls_pvalues.o \
alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o \
-@@ -72,45 +75,45 @@
+@@ -56,19 +59,19 @@
+ all: $(ALL)
- indexAllObj4 = $(indexObj0) $(indexObj4)
- ../bin/lastdb: $(indexAllObj4)
-- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj4) -lz
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj4) -lz
+ ../bin/lastdb: $(indexObj)
+- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexObj) -lz
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexObj) -lz
- indexAllObj5 = $(indexObj0) $(indexObj5)
- ../bin/lastdb5: $(indexAllObj5)
-- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj5) -lz
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj5) -lz
+ ../bin/lastal: $(alignObj)
+- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignObj) -lz
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignObj) -lz
- indexAllObj8 = $(indexObj0) $(indexObj8)
- ../bin/lastdb8: $(indexAllObj8)
-- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj8) -lz
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj8) -lz
-
- alignAllObj4 = $(alignObj0) $(alignObj4)
- ../bin/lastal: $(alignAllObj4)
-- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj4) -lz
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj4) -lz
-
- alignAllObj5 = $(alignObj0) $(alignObj5)
- ../bin/lastal5: $(alignAllObj5)
-- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj5) -lz
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj5) -lz
-
- alignAllObj8 = $(alignObj0) $(alignObj8)
- ../bin/lastal8: $(alignAllObj8)
-- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj8) -lz
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj8) -lz
-
- splitAllObj4 = $(splitObj0) $(splitObj4)
- ../bin/last-split: $(splitAllObj4)
-- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj4)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj4)
-
- splitAllObj5 = $(splitObj0) $(splitObj5)
- ../bin/last-split5: $(splitAllObj5)
-- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj5)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj5)
-
- splitAllObj8 = $(splitObj0) $(splitObj8)
- ../bin/last-split8: $(splitAllObj8)
-- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj8)
-+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj8)
+ ../bin/last-split: $(splitObj)
+- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitObj)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitObj)
../bin/last-pair-probs: $(PPOBJ)
- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $(PPOBJ) -lz
@@ -79,19 +47,19 @@ Description: Propagate variables to Makefile
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $(MBOBJ)
.SUFFIXES:
- .SUFFIXES: .o .c .cc .cpp .o5 .o8
-@@ -156,10 +159,10 @@
+ .SUFFIXES: .o .c .cc .cpp
+@@ -106,10 +109,10 @@
depend:
sed '/[m][v]/q' makefile > m
-- $(CXX) -MM -I. -std=c++11 *.cc | $(fix8) >> m
+- $(CXX) -MM -I. -std=c++11 *.cc >> m
- $(CC) -MM *.c >> m
- $(CXX) -MM alp/*.cpp | sed 's|.*:|alp/&|' >> m
-- $(CXX) -MM -I. split/*.cc | sed 's|.*:|split/&|' | $(fix8) >> m
-+ $(CXX) $(CPPFLAGS) -MM -I. -std=c++11 *.cc | $(fix8) >> m
+- $(CXX) -MM -I. split/*.cc | sed 's|.*:|split/&|' >> m
++ $(CXX) $(CPPFLAGS) -MM -I. -std=c++11 *.cc >> m
+ $(CC) $(CPPFLAGS) -MM *.c >> m
+ $(CXX) $(CPPFLAGS) -MM alp/*.cpp | sed 's|.*:|alp/&|' >> m
-+ $(CXX) $(CPPFLAGS) -MM -I. split/*.cc | sed 's|.*:|split/&|' | $(fix8) >> m
++ $(CXX) $(CPPFLAGS) -MM -I. split/*.cc | sed 's|.*:|split/&|' >> m
mv m makefile
- Alignment.o Alignment.o5 Alignment.o8: Alignment.cc Alignment.hh Centroid.hh GappedXdropAligner.hh \
+ Alignment.o: Alignment.cc Alignment.hh Centroid.hh GappedXdropAligner.hh \
mcf_big_seq.hh mcf_contiguous_queue.hh mcf_reverse_queue.hh \
=====================================
debian/patches/simde
=====================================
@@ -442,70 +442,30 @@ equivalents automatically
CXXFLAGS += -std=c++11
CXXFLAGS += -pthread -DHAS_CXX_THREAD
# -fomit-frame-pointer ?
-@@ -56,11 +55,12 @@
+@@ -52,25 +51,26 @@
PPOBJ = last-pair-probs.o last-pair-probs-main.o
MBOBJ = last-merge-batches.o
+SFX :=
--LAST4 = ../bin/lastdb ../bin/lastal ../bin/last-split
--LAST5 = ../bin/lastdb5 ../bin/lastal5 ../bin/last-split5
--LAST8 = ../bin/lastdb8 ../bin/lastal8 ../bin/last-split8
--ALL = $(LAST4) $(LAST5) ../bin/last-merge-batches ../bin/last-pair-probs
-+LAST4 = ../bin/lastdb$(SFX) ../bin/lastal$(SFX) ../bin/last-split$(SFX)
-+LAST5 = ../bin/lastdb5$(SFX) ../bin/lastal5$(SFX) ../bin/last-split5$(SFX)
-+LAST8 = ../bin/lastdb8$(SFX) ../bin/lastal8$(SFX) ../bin/last-split8$(SFX)
-+ALL = $(LAST4) $(LAST5) ../bin/last-merge-batches$(SFX) ../bin/last-pair-probs$(SFX)
+-ALL = ../bin/lastdb ../bin/lastal ../bin/last-split \
+-../bin/last-merge-batches ../bin/last-pair-probs
++ALL = ../bin/lastdb$(SFX) ../bin/lastal$(SFX) ../bin/last-split$(SFX) \
++../bin/last-merge-batches$(SFX) ../bin/last-pair-probs$(SFX)
- indexObj5 = $(indexObj4:.o=.o5)
- alignObj5 = $(alignObj4:.o=.o5)
-@@ -74,45 +74,45 @@
- last8: $(LAST8)
+ all: $(ALL)
- indexAllObj4 = $(indexObj0) $(indexObj4)
--../bin/lastdb: $(indexAllObj4)
-+../bin/lastdb$(SFX): $(indexAllObj4)
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj4) -lz
+-../bin/lastdb: $(indexObj)
++../bin/lastdb$(SFX): $(indexObj)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexObj) -lz
- indexAllObj5 = $(indexObj0) $(indexObj5)
--../bin/lastdb5: $(indexAllObj5)
-+../bin/lastdb5$(SFX): $(indexAllObj5)
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj5) -lz
+-../bin/lastal: $(alignObj)
++../bin/lastal$(SFX): $(alignObj)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignObj) -lz
- indexAllObj8 = $(indexObj0) $(indexObj8)
--../bin/lastdb8: $(indexAllObj8)
-+../bin/lastdb8$(SFX): $(indexAllObj8)
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj8) -lz
-
- alignAllObj4 = $(alignObj0) $(alignObj4)
--../bin/lastal: $(alignAllObj4)
-+../bin/lastal$(SFX): $(alignAllObj4)
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj4) -lz
-
- alignAllObj5 = $(alignObj0) $(alignObj5)
--../bin/lastal5: $(alignAllObj5)
-+../bin/lastal5$(SFX): $(alignAllObj5)
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj5) -lz
-
- alignAllObj8 = $(alignObj0) $(alignObj8)
--../bin/lastal8: $(alignAllObj8)
-+../bin/lastal8$(SFX): $(alignAllObj8)
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj8) -lz
-
- splitAllObj4 = $(splitObj0) $(splitObj4)
--../bin/last-split: $(splitAllObj4)
-+../bin/last-split$(SFX): $(splitAllObj4)
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj4)
-
- splitAllObj5 = $(splitObj0) $(splitObj5)
--../bin/last-split5: $(splitAllObj5)
-+../bin/last-split5$(SFX): $(splitAllObj5)
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj5)
-
- splitAllObj8 = $(splitObj0) $(splitObj8)
--../bin/last-split8: $(splitAllObj8)
-+../bin/last-split8$(SFX): $(splitAllObj8)
- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj8)
+-../bin/last-split: $(splitObj)
++../bin/last-split$(SFX): $(splitObj)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitObj)
-../bin/last-pair-probs: $(PPOBJ)
+../bin/last-pair-probs$(SFX): $(PPOBJ)
@@ -564,7 +524,7 @@ equivalents automatically
-#endif
--- a/src/Alignment.cc
+++ b/src/Alignment.cc
-@@ -365,12 +365,10 @@
+@@ -364,12 +364,10 @@
del.openCost, del.growCost,
ins.openCost, ins.growCost,
gap.pairCost, gap.isAffine, maxDrop, smMax)
@@ -577,7 +537,7 @@ equivalents automatically
: aligner.align(seq1 + start1, s2, isForward, globality, sm,
del.openCost, del.growCost,
ins.openCost, ins.growCost,
-@@ -387,14 +385,12 @@
+@@ -386,14 +384,12 @@
while( greedyAligner.getNextChunk( end1, end2, size ) )
chunks.push_back( SegmentPair( end1 - size, end2 - size, size ) );
}
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/a09af6b609cb9c773c564a974a8b94a5c5461f24
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/a09af6b609cb9c773c564a974a8b94a5c5461f24
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