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comparison ezBAMQC/src/htslib/htslib.mk @ 0:dfa3745e5fd8

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author youngkim
date Thu, 24 Mar 2016 17:12:52 -0400
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1 # Makefile rules useful for third-party code using htslib's public API.
2 #
3 # Copyright (C) 2013-2015 Genome Research Ltd.
4 #
5 # Author: John Marshall <jm18@sanger.ac.uk>
6 #
7 # Permission is hereby granted, free of charge, to any person obtaining a copy
8 # of this software and associated documentation files (the "Software"), to deal
9 # in the Software without restriction, including without limitation the rights
10 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11 # copies of the Software, and to permit persons to whom the Software is
12 # furnished to do so, subject to the following conditions:
13 #
14 # The above copyright notice and this permission notice shall be included in
15 # all copies or substantial portions of the Software.
16 #
17 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
20 # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 # DEALINGS IN THE SOFTWARE.
24
25 # The makefile fragment included below provides variables that can be used
26 # to express dependencies on headers supplied by an in-development htslib.
27 # If your source file foo.c #includes <htslib/hts.h> and <htslib/kstring.h>,
28 # you can write the correct prerequisites for foo.o as:
29 #
30 # HTSDIR = <path to htslib top-level directory>
31 # include $(HTSDIR)/htslib.mk
32 #
33 # foo.o: foo.c $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h
34 #
35 # Variables are not provided for k*.h, as those never include other headers.
36
37 HTSPREFIX = $(HTSDIR)/
38 include $(HTSDIR)/htslib_vars.mk
39
40 # Rules for rebuilding an in-development htslib's static and shared libraries.
41 # If your program foo links with libhts, adding the appropriate prerequisite
42 # will cause the library to be rebuilt as necessary:
43 #
44 # foo: foo.o $(HTSDIR)/libhts.a
45 #
46 # or similarly if your target requires any of the tools supplied:
47 #
48 # bar.bed.bgz.tbi: bar.bed.bgz $(HTSDIR)/tabix
49 # $(HTSDIR)/tabix -p bed bar.bed.bgz
50
51 HTSLIB_PUBLIC_HEADERS = \
52 $(HTSDIR)/htslib/bgzf.h \
53 $(HTSDIR)/htslib/faidx.h \
54 $(HTSDIR)/htslib/hfile.h \
55 $(HTSDIR)/htslib/hts.h \
56 $(HTSDIR)/htslib/hts_defs.h \
57 $(HTSDIR)/htslib/khash.h \
58 $(HTSDIR)/htslib/klist.h \
59 $(HTSDIR)/htslib/knetfile.h \
60 $(HTSDIR)/htslib/kseq.h \
61 $(HTSDIR)/htslib/ksort.h \
62 $(HTSDIR)/htslib/kstring.h \
63 $(HTSDIR)/htslib/regidx.h \
64 $(HTSDIR)/htslib/sam.h \
65 $(HTSDIR)/htslib/synced_bcf_reader.h \
66 $(HTSDIR)/htslib/tbx.h \
67 $(HTSDIR)/htslib/vcf.h \
68 $(HTSDIR)/htslib/vcf_sweep.h \
69 $(HTSDIR)/htslib/vcfutils.h
70
71 HTSLIB_ALL = \
72 $(HTSLIB_PUBLIC_HEADERS) \
73 $(HTSDIR)/bgzf.c \
74 $(HTSDIR)/faidx.c \
75 $(HTSDIR)/hfile_internal.h \
76 $(HTSDIR)/hfile.c \
77 $(HTSDIR)/hfile_irods.c \
78 $(HTSDIR)/hfile_net.c \
79 $(HTSDIR)/hts.c \
80 $(HTSDIR)/knetfile.c \
81 $(HTSDIR)/kstring.c \
82 $(HTSDIR)/regidx.c \
83 $(HTSDIR)/sam.c \
84 $(HTSDIR)/synced_bcf_reader.c \
85 $(HTSDIR)/tbx.c \
86 $(HTSDIR)/vcf.c \
87 $(HTSDIR)/vcf_sweep.c \
88 $(HTSDIR)/vcfutils.c \
89 $(HTSDIR)/cram/cram.h \
90 $(HTSDIR)/cram/cram_codecs.c \
91 $(HTSDIR)/cram/cram_codecs.h \
92 $(HTSDIR)/cram/cram_decode.c \
93 $(HTSDIR)/cram/cram_decode.h \
94 $(HTSDIR)/cram/cram_encode.c \
95 $(HTSDIR)/cram/cram_encode.h \
96 $(HTSDIR)/cram/cram_index.c \
97 $(HTSDIR)/cram/cram_index.h \
98 $(HTSDIR)/cram/cram_io.c \
99 $(HTSDIR)/cram/cram_io.h \
100 $(HTSDIR)/cram/cram_samtools.c \
101 $(HTSDIR)/cram/cram_samtools.h \
102 $(HTSDIR)/cram/cram_stats.c \
103 $(HTSDIR)/cram/cram_stats.h \
104 $(HTSDIR)/cram/cram_structs.h \
105 $(HTSDIR)/cram/files.c \
106 $(HTSDIR)/cram/mFILE.c \
107 $(HTSDIR)/cram/mFILE.h \
108 $(HTSDIR)/cram/md5.c \
109 $(HTSDIR)/cram/md5.h \
110 $(HTSDIR)/cram/misc.h \
111 $(HTSDIR)/cram/open_trace_file.c \
112 $(HTSDIR)/cram/open_trace_file.h \
113 $(HTSDIR)/cram/os.h \
114 $(HTSDIR)/cram/pooled_alloc.c \
115 $(HTSDIR)/cram/pooled_alloc.h \
116 $(HTSDIR)/cram/sam_header.c \
117 $(HTSDIR)/cram/sam_header.h \
118 $(HTSDIR)/cram/string_alloc.c \
119 $(HTSDIR)/cram/string_alloc.h \
120 $(HTSDIR)/cram/thread_pool.c \
121 $(HTSDIR)/cram/thread_pool.h \
122 $(HTSDIR)/cram/vlen.c \
123 $(HTSDIR)/cram/vlen.h \
124 $(HTSDIR)/cram/zfio.c \
125 $(HTSDIR)/cram/zfio.h
126
127 $(HTSDIR)/libhts.a: $(HTSLIB_ALL)
128 +cd $(HTSDIR) && $(MAKE) lib-static
129
130 $(HTSDIR)/libhts.so $(HTSDIR)/libhts.dylib: $(HTSLIB_ALL)
131 +cd $(HTSDIR) && $(MAKE) lib-shared
132
133 $(HTSDIR)/bgzip: $(HTSDIR)/bgzip.c $(HTSLIB_PUBLIC_HEADERS)
134 +cd $(HTSDIR) && $(MAKE) bgzip
135
136 $(HTSDIR)/htsfile: $(HTSDIR)/htsfile.c $(HTSLIB_PUBLIC_HEADERS)
137 +cd $(HTSDIR) && $(MAKE) htsfile
138
139 $(HTSDIR)/tabix: $(HTSDIR)/tabix.c $(HTSLIB_PUBLIC_HEADERS)
140 +cd $(HTSDIR) && $(MAKE) tabix
141
142 # Rules for phony targets. You may wish to have your corresponding phony
143 # targets invoke these in addition to their own recipes:
144 #
145 # clean: clean-htslib
146
147 clean-htslib install-htslib:
148 +cd $(HTSDIR) && $(MAKE) $(@:-htslib=)
149
150 .PHONY: clean-htslib install-htslib