1if HAVE_LIBMPI 2Parallel=Parallel 3endif 4 5if HAVE_PTHREAD 6GTest=vendor/gtest-1.7.0 7UnitTest=Unittest 8endif 9 10dist_doc_DATA = \ 11 ChangeLog \ 12 CITATION.bib CITATION.md \ 13 COPYRIGHT \ 14 LICENSE \ 15 README.md 16 17if HAVE_PANDOC 18dist_doc_DATA += README.html 19endif 20 21EXTRA_DIST=autogen.sh doxygen.conf 22 23SUBDIRS = \ 24 bin \ 25 doc \ 26 Common \ 27 Graph \ 28 DataLayer \ 29 DataBase \ 30 FMIndex \ 31 Assembly \ 32 dialign \ 33 Align \ 34 ABYSS $(Parallel) \ 35 Bloom \ 36 BloomDBG \ 37 Konnector \ 38 Consensus \ 39 DAssembler \ 40 DistanceEst \ 41 KAligner \ 42 Layout \ 43 LogKmerCount \ 44 Map \ 45 MergePaths \ 46 Overlap \ 47 PairedDBG \ 48 ParseAligns \ 49 PathOverlap \ 50 PopBubbles \ 51 Scaffold \ 52 SimpleGraph \ 53 kmerprint \ 54 FilterGraph \ 55 GapFiller \ 56 Sealer \ 57 RResolver \ 58 AdjList \ 59 vendor \ 60 $(GTest) \ 61 $(UnitTest) 62 63%.html: $(srcdir)/%.md 64 -pandoc -s -o $@ $< 65 66clean-local: 67 rm -f README.html 68 69clang-format: 70 for i in Bloom/RollingBloomDBGVisitor.h Bloom/bloom.cc BloomDBG/BloomIO.h \ 71 BloomDBG/Checkpoint.h BloomDBG/HashAgnosticCascadingBloom.h BloomDBG/bloom-dbg.* \ 72 ABYSS/abyss.cc Assembly/BranchGroup.h FMIndex/BitArrays.h FilterGraph/FilterGraph.cc \ 73 Graph/ContigGraphAlgorithms.h KAligner/Aligner.h KAligner/PipeMux.h Layout/layout.cc \ 74 MergePaths/MergeContigs.cpp MergePaths/MergePaths.cpp ParseAligns/ParseAligns.cpp \ 75 ParseAligns/abyss-fixmate.cc PathOverlap/PathOverlap.cpp PopBubbles/PopBubbles.cpp Scaffold/scaffold.cc \ 76 Unittest/BloomDBG/HashAgnosticCascadingBloomTest.cpp; do clang-format -style=file $$i >$$i.fixed; done 77 for i in Bloom/RollingBloomDBGVisitor.h Bloom/bloom.cc BloomDBG/BloomIO.h \ 78 BloomDBG/Checkpoint.h BloomDBG/HashAgnosticCascadingBloom.h BloomDBG/bloom-dbg.* \ 79 ABYSS/abyss.cc Assembly/BranchGroup.h FMIndex/BitArrays.h FilterGraph/FilterGraph.cc \ 80 Graph/ContigGraphAlgorithms.h KAligner/Aligner.h KAligner/PipeMux.h Layout/layout.cc \ 81 MergePaths/MergeContigs.cpp MergePaths/MergePaths.cpp ParseAligns/ParseAligns.cpp \ 82 ParseAligns/abyss-fixmate.cc PathOverlap/PathOverlap.cpp PopBubbles/PopBubbles.cpp Scaffold/scaffold.cc \ 83 Unittest/BloomDBG/HashAgnosticCascadingBloomTest.cpp; do diff -su $$i $$i.fixed && rm -f $$i.fixed; done 84 if ls *.fixed; then exit 1; fi 85