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