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