clean up better

 	$(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 \

	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