[med-svn] [Git][med-team/last-align][simde] clean up better

Michael R. Crusoe gitlab at salsa.debian.org
Fri Dec 20 16:20:56 GMT 2019 


Michael R. Crusoe pushed to branch simde at Debian Med / last-align


Commits:
7115000b by Michael R. Crusoe at 2019-12-20T16:19:23Z
clean up better

- - - - -


2 changed files:

- debian/patches/simde
- debian/rules


Changes:

=====================================
debian/patches/simde
=====================================
@@ -273,3 +273,146 @@
  	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $(MBOBJ)
  
  .SUFFIXES:
+@@ -147,9 +149,17 @@
+ 	mv m makefile
+ Alignment.o Alignment.o8: Alignment.cc Alignment.hh ScoreMatrixRow.hh SegmentPair.hh \
+  mcf_gap_costs.hh Alphabet.hh Centroid.hh GappedXdropAligner.hh \
+- mcf_contiguous_queue.hh mcf_simd.hh OneQualityScoreMatrix.hh \
+- mcf_substitution_matrix_stats.hh GeneticCode.hh GreedyXdropAligner.hh \
+- TwoQualityScoreMatrix.hh
++ mcf_contiguous_queue.hh mcf_simd.hh ../debian/include/simde/x86/avx2.h \
++ ../debian/include/simde/x86/avx.h ../debian/include/simde/x86/sse.h \
++ ../debian/include/simde/x86/mmx.h \
++ ../debian/include/simde/x86/../simde-common.h \
++ ../debian/include/simde/x86/../hedley.h \
++ ../debian/include/simde/x86/../check.h \
++ ../debian/include/simde/x86/../simde-arch.h \
++ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \
++ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \
++ OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh GeneticCode.hh \
++ GreedyXdropAligner.hh TwoQualityScoreMatrix.hh
+ AlignmentPot.o AlignmentPot.o8: AlignmentPot.cc AlignmentPot.hh Alignment.hh \
+  ScoreMatrixRow.hh SegmentPair.hh mcf_gap_costs.hh
+ AlignmentWrite.o AlignmentWrite.o8: AlignmentWrite.cc Alignment.hh ScoreMatrixRow.hh \
+@@ -160,28 +170,77 @@
+  Alphabet.hh
+ Alphabet.o Alphabet.o8: Alphabet.cc Alphabet.hh
+ Centroid.o Centroid.o8: Centroid.cc Centroid.hh GappedXdropAligner.hh \
+- mcf_contiguous_queue.hh mcf_simd.hh ScoreMatrixRow.hh mcf_gap_costs.hh \
+- SegmentPair.hh OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh \
++ mcf_contiguous_queue.hh mcf_simd.hh ../debian/include/simde/x86/avx2.h \
++ ../debian/include/simde/x86/avx.h ../debian/include/simde/x86/sse.h \
++ ../debian/include/simde/x86/mmx.h \
++ ../debian/include/simde/x86/../simde-common.h \
++ ../debian/include/simde/x86/../hedley.h \
++ ../debian/include/simde/x86/../check.h \
++ ../debian/include/simde/x86/../simde-arch.h \
++ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \
++ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \
++ ScoreMatrixRow.hh mcf_gap_costs.hh SegmentPair.hh \
++ OneQualityScoreMatrix.hh mcf_substitution_matrix_stats.hh \
+  GappedXdropAlignerInl.hh
+ CyclicSubsetSeed.o CyclicSubsetSeed.o8: CyclicSubsetSeed.cc CyclicSubsetSeed.hh \
+  CyclicSubsetSeedData.hh zio.hh mcf_zstream.hh stringify.hh
+ DiagonalTable.o DiagonalTable.o8: DiagonalTable.cc DiagonalTable.hh
+ GappedXdropAligner.o GappedXdropAligner.o8: GappedXdropAligner.cc GappedXdropAligner.hh \
+- mcf_contiguous_queue.hh mcf_simd.hh ScoreMatrixRow.hh \
+- GappedXdropAlignerInl.hh
++ mcf_contiguous_queue.hh mcf_simd.hh ../debian/include/simde/x86/avx2.h \
++ ../debian/include/simde/x86/avx.h ../debian/include/simde/x86/sse.h \
++ ../debian/include/simde/x86/mmx.h \
++ ../debian/include/simde/x86/../simde-common.h \
++ ../debian/include/simde/x86/../hedley.h \
++ ../debian/include/simde/x86/../check.h \
++ ../debian/include/simde/x86/../simde-arch.h \
++ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \
++ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \
++ ScoreMatrixRow.hh GappedXdropAlignerInl.hh
+ GappedXdropAligner2qual.o GappedXdropAligner2qual.o8: GappedXdropAligner2qual.cc \
+  GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_simd.hh \
++ ../debian/include/simde/x86/avx2.h ../debian/include/simde/x86/avx.h \
++ ../debian/include/simde/x86/sse.h ../debian/include/simde/x86/mmx.h \
++ ../debian/include/simde/x86/../simde-common.h \
++ ../debian/include/simde/x86/../hedley.h \
++ ../debian/include/simde/x86/../check.h \
++ ../debian/include/simde/x86/../simde-arch.h \
++ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \
++ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \
+  ScoreMatrixRow.hh GappedXdropAlignerInl.hh TwoQualityScoreMatrix.hh \
+  mcf_substitution_matrix_stats.hh
+ GappedXdropAligner3frame.o GappedXdropAligner3frame.o8: GappedXdropAligner3frame.cc \
+  GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_simd.hh \
++ ../debian/include/simde/x86/avx2.h ../debian/include/simde/x86/avx.h \
++ ../debian/include/simde/x86/sse.h ../debian/include/simde/x86/mmx.h \
++ ../debian/include/simde/x86/../simde-common.h \
++ ../debian/include/simde/x86/../hedley.h \
++ ../debian/include/simde/x86/../check.h \
++ ../debian/include/simde/x86/../simde-arch.h \
++ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \
++ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \
+  ScoreMatrixRow.hh GappedXdropAlignerInl.hh
+ GappedXdropAligner3framePssm.o GappedXdropAligner3framePssm.o8: GappedXdropAligner3framePssm.cc \
+  GappedXdropAligner.hh mcf_contiguous_queue.hh mcf_simd.hh \
++ ../debian/include/simde/x86/avx2.h ../debian/include/simde/x86/avx.h \
++ ../debian/include/simde/x86/sse.h ../debian/include/simde/x86/mmx.h \
++ ../debian/include/simde/x86/../simde-common.h \
++ ../debian/include/simde/x86/../hedley.h \
++ ../debian/include/simde/x86/../check.h \
++ ../debian/include/simde/x86/../simde-arch.h \
++ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \
++ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \
+  ScoreMatrixRow.hh GappedXdropAlignerInl.hh
+ GappedXdropAlignerPssm.o GappedXdropAlignerPssm.o8: GappedXdropAlignerPssm.cc GappedXdropAligner.hh \
+- mcf_contiguous_queue.hh mcf_simd.hh ScoreMatrixRow.hh \
+- GappedXdropAlignerInl.hh
++ mcf_contiguous_queue.hh mcf_simd.hh ../debian/include/simde/x86/avx2.h \
++ ../debian/include/simde/x86/avx.h ../debian/include/simde/x86/sse.h \
++ ../debian/include/simde/x86/mmx.h \
++ ../debian/include/simde/x86/../simde-common.h \
++ ../debian/include/simde/x86/../hedley.h \
++ ../debian/include/simde/x86/../check.h \
++ ../debian/include/simde/x86/../simde-arch.h \
++ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \
++ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \
++ ScoreMatrixRow.hh GappedXdropAlignerInl.hh
+ GeneticCode.o GeneticCode.o8: GeneticCode.cc GeneticCode.hh GeneticCodeData.hh \
+  Alphabet.hh zio.hh mcf_zstream.hh
+ GreedyXdropAligner.o GreedyXdropAligner.o8: GreedyXdropAligner.cc GreedyXdropAligner.hh \
+@@ -205,8 +264,9 @@
+  ScoreMatrixRow.hh qualityScoreUtil.hh stringify.hh
+ QualityPssmMaker.o QualityPssmMaker.o8: QualityPssmMaker.cc QualityPssmMaker.hh \
+  ScoreMatrixRow.hh qualityScoreUtil.hh stringify.hh
+-ScoreMatrix.o ScoreMatrix.o8: ScoreMatrix.cc ScoreMatrix.hh ScoreMatrixData.hh \
+- qualityScoreUtil.hh stringify.hh zio.hh mcf_zstream.hh
++ScoreMatrix.o ScoreMatrix.o8: ScoreMatrix.cc ScoreMatrix.hh ScoreMatrixRow.hh \
++ ScoreMatrixData.hh qualityScoreUtil.hh stringify.hh zio.hh \
++ mcf_zstream.hh
+ SegmentPair.o SegmentPair.o8: SegmentPair.cc SegmentPair.hh
+ SegmentPairPot.o SegmentPairPot.o8: SegmentPairPot.cc SegmentPairPot.hh SegmentPair.hh
+ SubsetMinimizerFinder.o SubsetMinimizerFinder.o8: SubsetMinimizerFinder.cc \
+@@ -245,11 +305,20 @@
+  alp/sls_falp_alignment_evaluer.hpp alp/sls_fsa1_pvalues.hpp \
+  GeneticCode.hh SubsetMinimizerFinder.hh SubsetSuffixArray.hh \
+  CyclicSubsetSeed.hh Centroid.hh GappedXdropAligner.hh \
+- mcf_contiguous_queue.hh mcf_simd.hh mcf_gap_costs.hh SegmentPair.hh \
+- AlignmentPot.hh Alignment.hh SegmentPairPot.hh ScoreMatrix.hh \
+- TantanMasker.hh tantan.hh DiagonalTable.hh GreedyXdropAligner.hh \
+- gaplessXdrop.hh gaplessPssmXdrop.hh gaplessTwoQualityXdrop.hh zio.hh \
+- mcf_zstream.hh threadUtil.hh version.hh
++ mcf_contiguous_queue.hh mcf_simd.hh ../debian/include/simde/x86/avx2.h \
++ ../debian/include/simde/x86/avx.h ../debian/include/simde/x86/sse.h \
++ ../debian/include/simde/x86/mmx.h \
++ ../debian/include/simde/x86/../simde-common.h \
++ ../debian/include/simde/x86/../hedley.h \
++ ../debian/include/simde/x86/../check.h \
++ ../debian/include/simde/x86/../simde-arch.h \
++ ../debian/include/simde/x86/sse2.h ../debian/include/simde/x86/sse4.1.h \
++ ../debian/include/simde/x86/ssse3.h ../debian/include/simde/x86/sse3.h \
++ mcf_gap_costs.hh SegmentPair.hh AlignmentPot.hh Alignment.hh \
++ SegmentPairPot.hh ScoreMatrix.hh TantanMasker.hh tantan.hh \
++ DiagonalTable.hh GreedyXdropAligner.hh gaplessXdrop.hh \
++ gaplessPssmXdrop.hh gaplessTwoQualityXdrop.hh zio.hh mcf_zstream.hh \
++ threadUtil.hh version.hh
+ lastdb.o lastdb.o8: lastdb.cc last.hh Alphabet.hh MultiSequence.hh \
+  ScoreMatrixRow.hh VectorOrMmap.hh Mmap.hh fileMap.hh stringify.hh \
+  SequenceFormat.hh qualityScoreUtil.hh LastdbArguments.hh \


=====================================
debian/rules
=====================================
@@ -37,14 +37,16 @@ ifeq (amd64,$(DEB_HOST_ARCH))
 	mkdir -p $(libexecdir)
 	for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \
 		$(MAKE) -j$(NUMJOBS) all SFX=-$${SIMD} CXXFLAGS="$(CXXFLAGS) -m$$SIMD" CFLAGS="$(CFLAGS) -m$$SIMD" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" ; \
-		rm src/*.o? ; \
+		find src -name '*.o' -delete ; \
+		find src -name '*.o8' -delete ; \
 	done
 else ifeq (i386,$(DEB_HOST_ARCH))
 	mkdir -p $(prefix)
 	mkdir -p $(libexecdir)
 	for SIMD in ssse3 sse3 sse2 sse mmx; do \
 		$(MAKE) -j$(NUMJOBS) all SFX=-$${SIMD} CXXFLAGS="$(CXXFLAGS) -m$$SIMD" CFLAGS="$(CFLAGS) -m$$SIMD" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" ; \
-		rm src/*.o? ; \
+		find src -name '*.o' -delete ; \
+		find src -name '*.o8' -delete ; \
 	done
 	$(MAKE) -j$(NUMJOBS) all SFX=-plain CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"
 else



View it on GitLab: https://salsa.debian.org/med-team/last-align/commit/7115000b993951a6922ba64a059a34edb4ec5b1e

-- 
View it on GitLab: https://salsa.debian.org/med-team/last-align/commit/7115000b993951a6922ba64a059a34edb4ec5b1e
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