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