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
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
|
# CMake script for Bio++ Sequence Library
# Author: Sylvain Gaillard and Julien Dutheil
# Created: 30/07/2012
# File list
SET(CPP_FILES
Bpp/Seq/Io/Fastq.cpp
Bpp/Seq/Io/Maf/MafParser.cpp
Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp
Bpp/Seq/Io/Maf/MafIterator.cpp
Bpp/Seq/Io/Maf/SequenceFilterMafIterator.cpp
Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.cpp
Bpp/Seq/Io/Maf/ChromosomeMafIterator.cpp
Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.cpp
Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp
Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp
Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp
Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp
Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp
Bpp/Seq/Io/Maf/QualityFilterMafIterator.cpp
Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp
Bpp/Seq/Io/Maf/OutputMafIterator.cpp
Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.cpp
Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp
Bpp/Seq/Io/Maf/MafSequence.cpp
Bpp/Seq/Io/Maf/MafStatistics.cpp
Bpp/Seq/Io/Maf/IterationListener.cpp
Bpp/Seq/Feature/SequenceFeature.cpp
Bpp/Seq/Feature/SequenceFeatureTools.cpp
Bpp/Seq/Feature/Gff/GffFeatureReader.cpp
Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp
)
SET(H_FILES
Bpp/Seq/Io/Fastq.h
Bpp/Seq/Io/Maf/MafSequence.h
Bpp/Seq/Io/Maf/MafParser.h
Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h
Bpp/Seq/Io/Maf/MafIterator.h
Bpp/Seq/Io/Maf/BlockLengthMafIterator.h
Bpp/Seq/Io/Maf/BlockSizeMafIterator.h
Bpp/Seq/Io/Maf/SequenceFilterMafIterator.h
Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h
Bpp/Seq/Io/Maf/ChromosomeMafIterator.h
Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.h
Bpp/Seq/Io/Maf/BlockMergerMafIterator.h
Bpp/Seq/Io/Maf/ConcatenateMafIterator.h
Bpp/Seq/Io/Maf/FullGapFilterMafIterator.h
Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h
Bpp/Seq/Io/Maf/EntropyFilterMafIterator.h
Bpp/Seq/Io/Maf/MaskFilterMafIterator.h
Bpp/Seq/Io/Maf/QualityFilterMafIterator.h
Bpp/Seq/Io/Maf/FeatureFilterMafIterator.h
Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h
Bpp/Seq/Io/Maf/OutputMafIterator.h
Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h
Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
Bpp/Seq/Io/Maf/MafStatistics.h
Bpp/Seq/Io/Maf/IterationListener.h
Bpp/Seq/Feature/SequenceFeature.h
Bpp/Seq/Feature/SequenceFeatureTools.h
Bpp/Seq/Feature/FeatureReader.h
Bpp/Seq/Feature/Gff/GffFeatureReader.h
Bpp/Seq/Feature/Gtf/GtfFeatureReader.h
)
# Build the static lib
ADD_LIBRARY(bppseqomics-static STATIC ${CPP_FILES})
SET_TARGET_PROPERTIES(bppseqomics-static
PROPERTIES OUTPUT_NAME bpp-seq-omics
CLEAN_DIRECT_OUTPUT 1
)
TARGET_LINK_LIBRARIES(bppseqomics-static ${LIBS})
# Build the shared lib
ADD_LIBRARY(bppseqomics-shared SHARED ${CPP_FILES})
SET_TARGET_PROPERTIES(bppseqomics-shared
PROPERTIES OUTPUT_NAME bpp-seq-omics
CLEAN_DIRECT_OUTPUT 1
VERSION ${BPPSEQOMICS_VERSION}
SOVERSION ${BPPSEQOMICS_VERSION_MAJOR}
)
TARGET_LINK_LIBRARIES(bppseqomics-shared ${LIBS})
# Install libs
INSTALL(TARGETS bppseqomics-static bppseqomics-shared DESTINATION lib${LIB_SUFFIX})
# Install headers
INSTALL(DIRECTORY Bpp/ DESTINATION include/Bpp FILES_MATCHING PATTERN "*.h")
# Generate generic include files (.all)
INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_SOURCE_DIR}/genIncludes.sh ${CMAKE_PREFIX_PATH}/include/Bpp)")
|
