c_cpp/lib/htslib/htslib.mk

   1 # Makefile rules useful for third-party code using htslib's public API.
   2 #
   3 #    Copyright (C) 2013-2016 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) $(htslib_kstring_h)
  34
  35 HTSPREFIX = $(HTSDIR)/
  36 include $(HTSDIR)/htslib_vars.mk
  37
  38 # Rules for rebuilding an in-development htslib's static and shared libraries.
  39 # If your program foo links with libhts, adding the appropriate prerequisite
  40 # will cause the library to be rebuilt as necessary:
  41 #
  42 #       foo: foo.o $(HTSDIR)/libhts.a
  43 #
  44 # or similarly if your target requires any of the tools supplied:
  45 #
  46 #       bar.bed.bgz.tbi: bar.bed.bgz $(HTSDIR)/tabix
  47 #               $(HTSDIR)/tabix -p bed bar.bed.bgz
  48
  49 HTSLIB_PUBLIC_HEADERS = \
  50         $(HTSDIR)/htslib/bgzf.h \
  51         $(HTSDIR)/htslib/cram.h \
  52         $(HTSDIR)/htslib/faidx.h \
  53         $(HTSDIR)/htslib/hfile.h \
  54         $(HTSDIR)/htslib/hts.h \
  55         $(HTSDIR)/htslib/hts_defs.h \
  56         $(HTSDIR)/htslib/hts_endian.h \
  57         $(HTSDIR)/htslib/hts_log.h \
  58         $(HTSDIR)/htslib/kbitset.h \
  59         $(HTSDIR)/htslib/kfunc.h \
  60         $(HTSDIR)/htslib/khash.h \
  61         $(HTSDIR)/htslib/khash_str2int.h \
  62         $(HTSDIR)/htslib/klist.h \
  63         $(HTSDIR)/htslib/knetfile.h \
  64         $(HTSDIR)/htslib/kseq.h \
  65         $(HTSDIR)/htslib/ksort.h \
  66         $(HTSDIR)/htslib/kstring.h \
  67         $(HTSDIR)/htslib/regidx.h \
  68         $(HTSDIR)/htslib/sam.h \
  69         $(HTSDIR)/htslib/synced_bcf_reader.h \
  70         $(HTSDIR)/htslib/tbx.h \
  71         $(HTSDIR)/htslib/thread_pool.h \
  72         $(HTSDIR)/htslib/vcf.h \
  73         $(HTSDIR)/htslib/vcf_sweep.h \
  74         $(HTSDIR)/htslib/vcfutils.h
  75
  76 HTSLIB_ALL = \
  77         $(HTSLIB_PUBLIC_HEADERS) \
  78         $(HTSDIR)/bcf_sr_sort.c \
  79         $(HTSDIR)/bcf_sr_sort.h \
  80         $(HTSDIR)/bgzf.c \
  81         $(HTSDIR)/config.h \
  82         $(HTSDIR)/errmod.c \
  83         $(HTSDIR)/faidx.c \
  84         $(HTSDIR)/hfile_internal.h \
  85         $(HTSDIR)/hfile.c \
  86         $(HTSDIR)/hfile_gcs.c \
  87         $(HTSDIR)/hfile_libcurl.c \
  88         $(HTSDIR)/hfile_net.c \
  89         $(HTSDIR)/hfile_s3.c \
  90         $(HTSDIR)/hts.c \
  91         $(HTSDIR)/hts_internal.h \
  92         $(HTSDIR)/kfunc.c \
  93         $(HTSDIR)/knetfile.c \
  94         $(HTSDIR)/kstring.c \
  95         $(HTSDIR)/md5.c \
  96         $(HTSDIR)/multipart.c \
  97         $(HTSDIR)/plugin.c \
  98         $(HTSDIR)/probaln.c \
  99         $(HTSDIR)/realn.c \
 100         $(HTSDIR)/regidx.c \
 101         $(HTSDIR)/sam.c \
 102         $(HTSDIR)/synced_bcf_reader.c \
 103         $(HTSDIR)/tbx.c \
 104         $(HTSDIR)/textutils.c \
 105         $(HTSDIR)/thread_pool.c \
 106         $(HTSDIR)/thread_pool_internal.h \
 107         $(HTSDIR)/vcf.c \
 108         $(HTSDIR)/vcf_sweep.c \
 109         $(HTSDIR)/vcfutils.c \
 110         $(HTSDIR)/cram/cram.h \
 111         $(HTSDIR)/cram/cram_codecs.c \
 112         $(HTSDIR)/cram/cram_codecs.h \
 113         $(HTSDIR)/cram/cram_decode.c \
 114         $(HTSDIR)/cram/cram_decode.h \
 115         $(HTSDIR)/cram/cram_encode.c \
 116         $(HTSDIR)/cram/cram_encode.h \
 117         $(HTSDIR)/cram/cram_external.c \
 118         $(HTSDIR)/cram/cram_index.c \
 119         $(HTSDIR)/cram/cram_index.h \
 120         $(HTSDIR)/cram/cram_io.c \
 121         $(HTSDIR)/cram/cram_io.h \
 122         $(HTSDIR)/cram/cram_samtools.c \
 123         $(HTSDIR)/cram/cram_samtools.h \
 124         $(HTSDIR)/cram/cram_stats.c \
 125         $(HTSDIR)/cram/cram_stats.h \
 126         $(HTSDIR)/cram/cram_structs.h \
 127         $(HTSDIR)/cram/files.c \
 128         $(HTSDIR)/cram/mFILE.c \
 129         $(HTSDIR)/cram/mFILE.h \
 130         $(HTSDIR)/cram/misc.h \
 131         $(HTSDIR)/cram/open_trace_file.c \
 132         $(HTSDIR)/cram/open_trace_file.h \
 133         $(HTSDIR)/cram/os.h \
 134         $(HTSDIR)/cram/pooled_alloc.c \
 135         $(HTSDIR)/cram/pooled_alloc.h \
 136         $(HTSDIR)/cram/rANS_byte.h \
 137         $(HTSDIR)/cram/rANS_static.c \
 138         $(HTSDIR)/cram/rANS_static.h \
 139         $(HTSDIR)/cram/sam_header.c \
 140         $(HTSDIR)/cram/sam_header.h \
 141         $(HTSDIR)/cram/string_alloc.c \
 142         $(HTSDIR)/cram/string_alloc.h
 143
 144 $(HTSDIR)/config.h:
 145         +cd $(HTSDIR) && $(MAKE) config.h
 146
 147 $(HTSDIR)/libhts.a: $(HTSLIB_ALL)
 148         +cd $(HTSDIR) && $(MAKE) lib-static
 149
 150 $(HTSDIR)/libhts.so $(HTSDIR)/libhts.dylib: $(HTSLIB_ALL)
 151         +cd $(HTSDIR) && $(MAKE) lib-shared
 152
 153 $(HTSDIR)/bgzip: $(HTSDIR)/bgzip.c $(HTSLIB_PUBLIC_HEADERS)
 154         +cd $(HTSDIR) && $(MAKE) bgzip
 155
 156 $(HTSDIR)/htsfile: $(HTSDIR)/htsfile.c $(HTSLIB_PUBLIC_HEADERS)
 157         +cd $(HTSDIR) && $(MAKE) htsfile
 158
 159 $(HTSDIR)/tabix: $(HTSDIR)/tabix.c $(HTSLIB_PUBLIC_HEADERS)
 160         +cd $(HTSDIR) && $(MAKE) tabix
 161
 162 $(HTSDIR)/htslib_static.mk: $(HTSDIR)/htslib.pc.tmp
 163         +cd $(HTSDIR) && $(MAKE) htslib_static.mk
 164
 165 $(HTSDIR)/htslib.pc.tmp:
 166         +cd $(HTSDIR) && $(MAKE) htslib.pc.tmp
 167
 168 # Rules for phony targets.  You may wish to have your corresponding phony
 169 # targets invoke these in addition to their own recipes:
 170 #
 171 #       clean: clean-htslib
 172
 173 all-htslib clean-htslib install-htslib plugins-htslib:
 174         +cd $(HTSDIR) && $(MAKE) $(@:-htslib=)
 175
 176 .PHONY: all-htslib clean-htslib install-htslib plugins-htslib