1# =========================================================================== 2# 3# PUBLIC DOMAIN NOTICE 4# National Center for Biotechnology Information 5# 6# This software/database is a "United States Government Work" under the 7# terms of the United States Copyright Act. It was written as part of 8# the author's official duties as a United States Government employee and 9# thus cannot be copyrighted. This software/database is freely available 10# to the public for use. The National Library of Medicine and the U.S. 11# Government have not placed any restriction on its use or reproduction. 12# 13# Although all reasonable efforts have been taken to ensure the accuracy 14# and reliability of the software and data, the NLM and the U.S. 15# Government do not and cannot warrant the performance or results that 16# may be obtained by using this software or data. The NLM and the U.S. 17# Government disclaim all warranties, express or implied, including 18# warranties of performance, merchantability or fitness for any particular 19# purpose. 20# 21# Please cite the author in any work or product based on this material. 22# 23# =========================================================================== 24 25 26default: std 27 28TOP ?= $(abspath ../..) 29MODULE = libs/axf 30 31INT_LIBS = \ 32 libaxf \ 33 libwaxf 34 35ALL_LIBS = \ 36 $(INT_LIBS) 37 38OBJFILES = \ 39 $(AXF_OBJ) \ 40 $(WAXF_OBJ) 41 42include $(TOP)/build/Makefile.env 43 44#------------------------------------------------------------------------------- 45# outer targets 46# 47all std: makedirs compile 48 @ $(MAKE_CMD) $(TARGDIR)/std 49 50$(ALL_LIBS): makedirs 51 @ $(MAKE_CMD) $(TARGDIR)/$@ 52 53.PHONY: all std $(ALL_LIBS) 54 55#------------------------------------------------------------------------------- 56# std 57# 58$(TARGDIR)/std: \ 59 $(addprefix $(TARGDIR)/,$(ALL_LIBS)) 60 61.PHONY: $(TARGDIR)/all $(TARGDIR)/std 62 63#------------------------------------------------------------------------------- 64# clean 65# 66clean: stdclean 67 68.PHONY: clean 69 70#------------------------------------------------------------------------------- 71# alignment transform library 72# 73$(TARGDIR)/libaxf: $(addprefix $(ILIBDIR)/libaxf.,$(ILIBEXT)) 74 75AXF_SRC = \ 76 ref-tbl-sub-select \ 77 ref-restore-read \ 78 align-restore-read \ 79 raw-restore-read \ 80 raw-restore-qual \ 81 seq-restore-read \ 82 seq-restore-linkage-group \ 83 seq-construct-read \ 84 cigar \ 85 project_read_from_sequence \ 86 not-my-row \ 87 template-len \ 88 get-sam-flags \ 89 align-ref-pos \ 90 align-ref-name \ 91 align-ref-seq-id \ 92 align-local_ref_id \ 93 align-local_ref_start \ 94 generate-mismatch-qual \ 95 mismatch-restore-qual \ 96 ref-preserve_qual \ 97 ref-tbl \ 98 make-cmp-read_desc \ 99 get_mate_align_ids \ 100 range-list \ 101 refseq \ 102 wgs \ 103 restore-read 104 105AXF_OBJ = \ 106 $(addsuffix .$(LOBX),$(AXF_SRC)) 107 108AXF_LIB = \ 109 -lalign-reader \ 110 -dvdb \ 111 -dkdb \ 112 -dklib \ 113 -dm \ 114 -dz 115 116$(ILIBDIR)/libaxf.$(LIBX): $(AXF_OBJ) 117 $(LD) --slib -o $@ $^ $(AXF_LIB) 118 119 120#------------------------------------------------------------------------------- 121# alignment transform update library 122# 123$(TARGDIR)/libwaxf: $(addprefix $(ILIBDIR)/libwaxf.,$(ILIBEXT)) 124 125WAXF_SRC = \ 126 $(AXF_SRC) \ 127 refseq-stats 128 129WAXF_OBJ = \ 130 $(addsuffix .$(LOBX),$(WAXF_SRC)) 131 132WAXF_LIB = \ 133 -lalign-reader \ 134 -dwvdb \ 135 -dwkdb \ 136 -lkfg \ 137 -dklib \ 138 -dm \ 139 -dz 140 141$(ILIBDIR)/libwaxf.$(LIBX): $(WAXF_OBJ) 142 $(LD) --slib -o $@ $^ $(WAXF_LIB) 143 144compile: stdcompile 145 146$(TARGDIR)/compile: $(OBJFILES) 147 148#------------------------------------------------------------------------------- 149# fuzz 150# 151fuzz: std 152 cp $(addsuffix .$(LIBX),$(addprefix $(ILIBDIR)/,$(INT_LIBS))) $(FLIBDIR)/ 153