-
Notifications
You must be signed in to change notification settings - Fork 195
/
Makefile
1089 lines (926 loc) · 61.4 KB
/
Makefile
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
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
DEP_DIR:=./deps
SRC_DIR:=src
ALGORITHMS_SRC_DIR:=$(SRC_DIR)/algorithms
CONFIG_SRC_DIR:=$(SRC_DIR)/config
IO_SRC_DIR:=$(SRC_DIR)/io
SUBCOMMAND_SRC_DIR:=$(SRC_DIR)/subcommand
UNITTEST_SRC_DIR:=$(SRC_DIR)/unittest
UNITTEST_SUPPORT_SRC_DIR:=$(SRC_DIR)/unittest/support
BIN_DIR:=bin
UNITTEST_BIN_DIR:=$(BIN_DIR)/unittest
OBJ_DIR:=obj
SHARED_OBJ_DIR:=obj/pic
ALGORITHMS_OBJ_DIR:=$(OBJ_DIR)/algorithms
ALGORITHMS_SHARED_OBJ_DIR:=$(SHARED_OBJ_DIR)/algorithms
CONFIG_OBJ_DIR:=$(OBJ_DIR)/config
IO_OBJ_DIR:=$(OBJ_DIR)/io
IO_SHARED_OBJ_DIR:=$(SHARED_OBJ_DIR)/io
SUBCOMMAND_OBJ_DIR:=$(OBJ_DIR)/subcommand
UNITTEST_OBJ_DIR:=$(OBJ_DIR)/unittest
UNITTEST_SUPPORT_OBJ_DIR:=$(OBJ_DIR)/unittest/support
LIB_DIR:=lib
# INC_DIR must be a relative path
INC_DIR:=include
CWD:=$(shell pwd)
PKG_CONFIG ?= pkg-config
SFX :=
EXE:=vg$(SFX)
# Expose compiler we want to use to all build commands as an environment variable.
export CC CXX
all: $(BIN_DIR)/$(EXE)
# Magic dependencies (see <http://make.mad-scientist.net/papers/advanced-auto-dependency-generation/#tldr>)
include $(wildcard $(OBJ_DIR)/*.d)
include $(wildcard $(SHARED_OBJ_DIR)/*.d)
include $(wildcard $(ALGORITHMS_OBJ_DIR)/*.d)
include $(wildcard $(ALGORITHMS_SHARED_OBJ_DIR)/*.d)
include $(wildcard $(CONFIG_OBJ_DIR)/*.d)
include $(wildcard $(IO_OBJ_DIR)/*.d)
include $(wildcard $(IO_SHARED_OBJ_DIR)/*.d)
include $(wildcard $(SUBCOMMAND_OBJ_DIR)/*.d)
include $(wildcard $(UNITTEST_OBJ_DIR)/*.d)
include $(wildcard $(UNITTEST_BIN_DIR)/*.d)
# What pkg-config-controlled system dependencies should we use compile and link flags from?
# Use PKG_CONFIG_PATH to point the build system at the right versions of these, if they aren't picked up automatically.
# We can't do this for our bundled, pkg-config-supporting dependencies (like htslib) because they won't be built yet.
PKG_CONFIG_DEPS := cairo libzstd
# These are like PKG_CONFIG_DEPS but we try to always link them statically, if possible.
# Note that we then must *always* link anything *else* that uses them statically.
# Jansson has to be in here because it has to come after libvgio, which is in the static deps.
PKG_CONFIG_STATIC_DEPS := protobuf jansson
# We don't ask for -fopenmp here because how we get it can depend on the compiler.
# We don't ask for automatic Make dependency file (*.d) generation here because
# the options we pass can interfere with similar options in dependency project.
CXXFLAGS := -O3 -Werror=return-type -ggdb -g $(CXXFLAGS)
# Keep dependency generation flags for just our own sources
DEPGEN_FLAGS := -MMD -MP
# Set include flags. All -I options need to go in here, so the first directory
# listed is genuinely searched first.
# Also, Protobuf produces an absurd number of pkg-config flags now, so we deduplicate them
# even though that's not *always* safe. See
# <https://stackoverflow.com/a/11532197> and
# <https://github.com/protocolbuffers/protobuf/issues/12998>
INCLUDE_FLAGS :=-I$(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(UNITTEST_SUPPORT_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) | tr ' ' '\n' | awk '!x[$$0]++' | tr '\n' ' ')
# Define libraries to link vg against.
# These need to come before library search paths from LDFLAGS or we won't
# prefer linking vg-installed dependencies over system ones.
LD_LIB_DIR_FLAGS := -L$(CWD)/$(LIB_DIR)
LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -lkff -ldivsufsort -ldivsufsort64 -lvcfh -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lbdsg -lxg -lsdsl -lzstd -lhandlegraph
# We omit Boost Program Options for now; we find it in a platform-dependent way.
# By default it has no suffix
BOOST_SUFFIX=""
# We define some more libraries to link against at the end, in static linking mode if possible, so we can use faster non-PIC code. These have both .so/.dylib and .a versions available.
LD_STATIC_LIB_FLAGS := -lvgio -lhts -ldeflate -lz -lbz2 -llzma
# Some of our static libraries depend on libraries that may not always be avilable in static form.
LD_STATIC_LIB_DEPS := -lpthread -lm
# Use pkg-config to find dependencies.
# Always use --static so that we have the -l flags for transitive dependencies, in case we're doing a full static build.
# But only force static linking of the dependencies we want to use non-PIC code for, for speed.
LD_LIB_FLAGS += $(shell $(PKG_CONFIG) --libs --static $(PKG_CONFIG_DEPS))
LD_STATIC_LIB_FLAGS += $(shell $(PKG_CONFIG) --libs --static $(PKG_CONFIG_STATIC_DEPS))
# Some libraries need to be linked only into the binary
LD_EXE_LIB_FLAGS :=
# We also use plain LDFLAGS to point at system library directories that we want
# to propagate through to dependencies' builds.
# CMake builds that need to find OpenMP might not know about all the prefixes it could be installed into.
# So we make a list of prefixes to search for it.
OMP_PREFIXES:=/
COMPILER_ID=$(strip $(shell $(CXX) --version 2>&1))
ifeq ($(shell uname -s),Darwin)
$(info OS is Mac)
# Don't try and set an rpath on any dependency utilities because that's not
# a thing and install names will work.
LD_UTIL_RPATH_FLAGS=""
# Homebrew installs a Protobuf that uses an Abseil that is built with C++17, so we need to build with at least C++17
CXX_STANDARD?=17
# We may need libraries from Macports
ifeq ($(shell if [ -d /opt/local/lib ];then echo 1;else echo 0;fi), 1)
# Use /opt/local/lib if present when building dependencies
LDFLAGS += -L/opt/local/lib
endif
ifeq ($(shell if [ -d /usr/local/lib ];then echo 1;else echo 0;fi), 1)
# Use /usr/local/lib if present.
LDFLAGS += -L/usr/local/lib
endif
ifeq ($(shell if [ -d /usr/local/include ];then echo 1;else echo 0;fi), 1)
# Use /usr/local/include to the end of the include search path.
# Make sure it is system level only so it comes after other -I paths.
INCLUDE_FLAGS += -isystem /usr/local/include
ifeq ($(shell if [ -d /usr/local/include/cairo ];then echo 1;else echo 0;fi), 1)
# pkg-config is not always smart enough to find Cairo's include path for us.
# We make sure to grab its directory manually if we see it.
INCLUDE_FLAGS += -isystem /usr/local/include/cairo
LD_LIB_FLAGS += -lcairo
endif
endif
ifndef HOMEBREW_PREFIX
BREW_PATH=$(shell which brew 2>/dev/null)
ifneq ($(BREW_PATH),)
# Get prefix from Homebrew instead of environment
HOMEBREW_PREFIX=$(shell brew --prefix)
endif
endif
ifdef HOMEBREW_PREFIX
# We need Bison from Homebrew instead of Apple's old Bison, and GNU coreutils
export PATH:=$(HOMEBREW_PREFIX)/opt/bison/bin:$(HOMEBREW_PREFIX)/opt/coreutils/libexec/gnubin:$(PATH)
# If we have homebrew, use Homebrew in general
CXXFLAGS += -I$(HOMEBREW_PREFIX)/include
LDFLAGS += -L$(HOMEBREW_PREFIX)/lib
endif
# We need to find Boost Program Options. It is usually
# -lboost_program_options, except for on Macports installs of Boost where
# it is -lboost_program_options-mt. If we were a real build system we would
# try things until it worked. Instead, we guess.
ifeq ($(shell if [ -f /opt/local/lib/libboost_program_options-mt.dylib ];then echo 1;else echo 0;fi), 1)
# This is where Macports puts it, so use that name
BOOST_SUFFIX="-mt"
endif
# Our compiler might be Apple clang, which doesn't have -fopenmp.
ifneq ($(strip $(shell echo "$(COMPILER_ID)" | grep -i clang | wc -l)), 0)
# This is Clang.
$(info Compiler $(CXX) is Clang)
# We need to use the hard way of getting OpenMP not bundled with the compiler.
# The compiler only needs to do the preprocessing
CXXFLAGS += -Xpreprocessor -fopenmp
ifeq ($(shell if [ -e $(HOMEBREW_PREFIX)/include/omp.h ]; then echo 1; else echo 0; fi), 1)
# libomp used to be globally installed in Homebrew
$(info OMP source is Homebrew libomp global install)
OMP_PREFIXES:=$(OMP_PREFIXES);$(HOMEBREW_PREFIX)
else ifeq ($(shell if [ -d $(HOMEBREW_PREFIX)/opt/libomp/include ]; then echo 1; else echo 0; fi), 1)
# libomp moved to these directories, recently, because it is now keg-only to not fight GCC
$(info OMP source is Homebrew libomop keg)
CXXFLAGS += -I$(HOMEBREW_PREFIX)/opt/libomp/include
LDFLAGS += -L$(HOMEBREW_PREFIX)/opt/libomp/lib
OMP_PREFIXES:=$(OMP_PREFIXES);$(HOMEBREW_PREFIX)/opt/libomp
else ifeq ($(shell if [ -d /opt/local/lib/libomp ]; then echo 1; else echo 0; fi), 1)
# Macports installs libomp to /opt/local/lib/libomp
$(info OMP source Macports)
CXXFLAGS += -I/opt/local/include/libomp
LDFLAGS += -L/opt/local/lib/libomp
OMP_PREFIXES:=$(OMP_PREFIXES);/opt/local
else
$(error OMP is not available from either Homebrew or Macports)
endif
# We also need to link it
LD_LIB_FLAGS += -lomp
else
$(info Compiler $(CXX) is GCC)
# The compiler is (probably?) GNU GCC
# On Mac, we need to make sure to configure it to use libc++ like
# Clang, and not GNU libstdc++.
# Otherwise, we won't be able to use any C++ system libraries from
# Homebrew or Macports, which will be built against libc++.
# See https://stackoverflow.com/q/22228208
CXXFLAGS += -fopenmp
# Find includes using Clang
LIBCXX_INCLUDES := $(shell clang++ -print-search-dirs | perl -ne 's{^libraries: =(.*)}{$$1/../../../} && print')
# Use them and libc++ and not the normal standard library
CXXFLAGS := -isystem $(LIBCXX_INCLUDES)/include/c++/v1 -nostdinc++ -nodefaultlibs -lc -lc++ -lc++abi -lgcc_s.1 -Wl,-no_compact_unwind $(CXXFLAGS)
# Make sure to use the right libgomp to go with libomp
LD_LIB_FLAGS += -lomp -lgomp.1
endif
# We care about building only for the current machine. If we do something
# more restrictive we can have trouble inlining parts of the standard
# library that were built for something less restrictive. However,
# Apple Clang does not recognize -march=native on ARM.
ifeq ($(shell uname -m), x86_64)
CXXFLAGS += -march=native
endif
# Note shared libraries are dylibs
SHARED_SUFFIX = dylib
# Define options to start static linking of libraries.
# We don't actually do any static linking on Mac, so we leave this empty.
START_STATIC =
END_STATIC =
# We need to use special flags to let us rename libraries.
# See <https://github.com/Homebrew/legacy-homebrew/issues/20233>
LD_RENAMEABLE_FLAGS = -Wl,-headerpad_max_install_names
else
# We are not running on OS X
$(info OS is Linux)
$(info Compiler $(CXX) is assumed to be GCC)
# Linux can have some old compilers so we want to work back to C++14
CXX_STANDARD?=14
# Set an rpath for vg and dependency utils to find installed libraries
LD_UTIL_RPATH_FLAGS="-Wl,-rpath,$(CWD)/$(LIB_DIR)"
LD_LIB_FLAGS += $(LD_UTIL_RPATH_FLAGS)
# Make sure to allow backtrace access to all our symbols, even those which are not exported.
# Absolutely no help in a static build.
LD_LIB_FLAGS += -rdynamic
# We want to link against the elfutils libraries
LD_LIB_FLAGS += -ldwfl -ldw -ldwelf -lelf -lebl
# We want to link against libatomic which the GNU C++ standard library needs.
# See <https://github.com/nodejs/node/issues/30093> and <https://stackoverflow.com/q/30591313>
LD_LIB_FLAGS += -latomic
# We get OpenMP the normal way, using whatever the compiler knows about
CXXFLAGS += -fopenmp
ifeq ($(shell arch), x86_64)
# We care about building for SSE4.2 only and not AVX, to have vaguely portable binaries
CXXFLAGS += -msse4.2
endif
# Note shared libraries are so files
SHARED_SUFFIX = so
# Define options to start static linking of libraries on GNU ld.
START_STATIC = -Wl,-Bstatic
# Note that END_STATIC is only safe to use in a mostly-dynamic build, and has to appear or we will try to statically link secret trailing libraries.
END_STATIC = -Wl,-Bdynamic
# We don't need any flags because we don't need to rename libraries with install_name_tool
LD_RENAMEABLE_FLAGS =
endif
# Set the C++ standard we are using
CXXFLAGS := -std=c++$(CXX_STANDARD) $(CXXFLAGS)
# Propagate CXXFLAGS and LDFLAGS to child makes and other build processes
export CXXFLAGS
$(info CXXFLAGS are $(CXXFLAGS))
export LDFLAGS
$(info LDFLAGS are $(LDFLAGS))
OMP_MISSING=$(strip $(shell echo \\\#include \<omp.h\> | $(CXX) $(CXXFLAGS) -x c++ -E /dev/stdin -o /dev/null 2>&1 | head -n1 | grep error | wc -l))
ifeq ($(OMP_MISSING), 1)
$(warning OpenMP header omp.h is not available! vg will not be able to build!)
endif
# Actually set the Boost library option, with the determined suffix
LD_LIB_FLAGS += "-lboost_program_options$(BOOST_SUFFIX)"
# These libs need to come after libdw if used, because libdw depends on them
LD_LIB_FLAGS += -ldl -llzma -lbz2 -lzstd
# Sometimes we need to filter the assembler output. The assembler can run during
# ./configure scripts, compiler calls, or $(MAKE) calls (other than $(MAKE)
# install). So we just stick $(FILTER) at the end of all such commands.
ifeq ($(shell uname -s),Darwin)
# We need to apply a filter to all our build command output. This discards
# all the assembler warnings which can overwhelm Travis log storage.
FILTER=2>&1 | python3 $(CWD)/scripts/filter-noisy-assembler-warnings.py
# For the filter to work and not just swallow errors we also need to turn on
# pipefail in the shell
SHELL=/bin/bash -o pipefail
else
# No filter
FILTER=
endif
# When building statically, we need to tell the linker not to bail if it sees multiple definitions.
# libc on e.g. our Jenkins host does not define malloc as weak, so other mallocs can't override it in a static build.
# TODO: Why did this problem only begin to happen when libvw was added?
STATIC_FLAGS=-static -static-libstdc++ -static-libgcc -Wl,--allow-multiple-definition
# These are put into libvg. Grab everything except main
OBJ = $(filter-out $(OBJ_DIR)/main.o,$(patsubst $(SRC_DIR)/%.cpp,$(OBJ_DIR)/%.o,$(wildcard $(SRC_DIR)/*.cpp)))
SHARED_OBJ = $(patsubst $(OBJ_DIR)/%.o,$(SHARED_OBJ_DIR)/%.o,$(OBJ))
# And all the algorithms
ALGORITHMS_OBJ = $(patsubst $(ALGORITHMS_SRC_DIR)/%.cpp,$(ALGORITHMS_OBJ_DIR)/%.o,$(wildcard $(ALGORITHMS_SRC_DIR)/*.cpp))
ALGORITHMS_SHARED_OBJ = $(patsubst $(ALGORITHMS_OBJ_DIR)/%.o,$(ALGORITHMS_SHARED_OBJ_DIR)/%.o,$(ALGORITHMS_OBJ))
# These aren't put into libvg. They are linked into vg itself to communicate
# things about the platform.
# Config objects are built individually and conditionally; that's the point.
CONFIG_OBJ =
# But always build all the IO logic
IO_OBJ = $(patsubst $(IO_SRC_DIR)/%.cpp,$(IO_OBJ_DIR)/%.o,$(wildcard $(IO_SRC_DIR)/*.cpp))
IO_SHARED_OBJ = $(patsubst $(IO_OBJ_DIR)/%.o,$(IO_SHARED_OBJ_DIR)/%.o,$(IO_OBJ))
# These aren't put into libvg, but they provide subcommand implementations for the vg bianry
SUBCOMMAND_OBJ = $(patsubst $(SUBCOMMAND_SRC_DIR)/%.cpp,$(SUBCOMMAND_OBJ_DIR)/%.o,$(wildcard $(SUBCOMMAND_SRC_DIR)/*.cpp))
# These aren't put into libvg. But they do go into the main vg binary to power its self-test.
UNITTEST_OBJ = $(patsubst $(UNITTEST_SRC_DIR)/%.cpp,$(UNITTEST_OBJ_DIR)/%.o,$(wildcard $(UNITTEST_SRC_DIR)/*.cpp))
# These support the tests. Some should go into the main vg binary but some should only go into test-suite binaries.
UNITTEST_SUPPORT_OBJ = $(patsubst $(UNITTEST_SUPPORT_SRC_DIR)/%.cpp,$(UNITTEST_SUPPORT_OBJ_DIR)/%.o,$(wildcard $(UNITTEST_SUPPORT_SRC_DIR)/*.cpp))
# These are per-test-suite binaries we can build faster
UNITTEST_EXE = $(patsubst $(UNITTEST_SRC_DIR)/%.cpp,$(UNITTEST_BIN_DIR)/%,$(wildcard $(UNITTEST_SRC_DIR)/*.cpp))
RAPTOR_DIR:=deps/raptor
JEMALLOC_DIR:=deps/jemalloc
LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc
SDSL_DIR:=deps/sdsl-lite
SNAPPY_DIR:=deps/snappy
GCSA2_DIR:=deps/gcsa2
GBWT_DIR:=deps/gbwt
GBWTGRAPH_DIR=deps/gbwtgraph
KFF_DIR=deps/kff-cpp-api
PROGRESS_BAR_DIR:=deps/progress_bar
FASTAHACK_DIR:=deps/fastahack
FERMI_DIR:=deps/fermi-lite
VCFLIB_DIR:=deps/vcflib
TABIXPP_DIR:=deps/tabixpp
HTSLIB_DIR:=deps/htslib
GSSW_DIR:=deps/gssw
SPARSEHASH_DIR:=deps/sparsehash
SPARSEPP_DIR:=deps/sparsepp
SHA1_DIR:=deps/sha1
DYNAMIC_DIR:=deps/DYNAMIC
SSW_DIR:=deps/ssw/src
LINLS_DIR:=deps/sublinear-Li-Stephens
STRUCTURES_DIR:=deps/structures
BACKWARD_CPP_DIR:=deps/backward-cpp
DOZEU_DIR:=deps/dozeu
ELFUTILS_DIR:=deps/elfutils
LIBDEFLATE_DIR:=deps/libdeflate
LIBVGIO_DIR:=deps/libvgio
LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
LIBBDSG_DIR:=deps/libbdsg
XG_DIR:=deps/xg
MMMULTIMAP_DIR=deps/mmmultimap
IPS4O_DIR=deps/ips4o
BBHASH_DIR=deps/BBHash
MIO_DIR=deps/mio
ATOMIC_QUEUE_DIR=deps/atomic_queue
# Dependencies that go into libvg's archive
# These go in libvg but come from dependencies
DEP_OBJ =
DEP_OBJ += $(OBJ_DIR)/progress_bar.o
DEP_OBJ += $(OBJ_DIR)/sha1.o
DEP_OBJ += $(OBJ_DIR)/Fasta.o
DEP_SHARED_OBJ = $(patsubst $(OBJ_DIR)/%.o,$(SHARED_OBJ_DIR)/%.o,$(DEP_OBJ))
# These are libraries that we need to build before we link vg.
# It would be nice to dump their contents into libvg to make it stand-alone.
# But that requires fancy ar scripting.
# If you just pass them to ar it puts the library *file* in libvg where nothing can read it.
LIB_DEPS =
LIB_DEPS += $(LIB_DIR)/libsdsl.a
LIB_DEPS += $(LIB_DIR)/libssw.a
LIB_DEPS += $(LIB_DIR)/libsnappy.a
LIB_DEPS += $(LIB_DIR)/libgcsa2.a
LIB_DEPS += $(LIB_DIR)/libgbwt.a
LIB_DEPS += $(LIB_DIR)/libgbwtgraph.a
LIB_DEPS += $(LIB_DIR)/libkff.a
LIB_DEPS += $(LIB_DIR)/libhts.a
LIB_DEPS += $(LIB_DIR)/libtabixpp.a
LIB_DEPS += $(LIB_DIR)/libvcflib.a
LIB_DEPS += $(LIB_DIR)/libgssw.a
LIB_DEPS += $(LIB_DIR)/libvcfh.a
LIB_DEPS += $(LIB_DIR)/libsonlib.a
LIB_DEPS += $(LIB_DIR)/libpinchesandcacti.a
LIB_DEPS += $(LIB_DIR)/libraptor2.a
LIB_DEPS += $(LIB_DIR)/libfml.a
LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
LIB_DEPS += $(LIB_DIR)/libstructures.a
LIB_DEPS += $(LIB_DIR)/libdeflate.a
LIB_DEPS += $(LIB_DIR)/libvgio.a
LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
LIB_DEPS += $(LIB_DIR)/libbdsg.a
LIB_DEPS += $(LIB_DIR)/libxg.a
ifneq ($(shell uname -s),Darwin)
# On non-Mac (i.e. Linux), where ELF binaries are used, pull in libdw which
# backward-cpp will use.
LIB_DEPS += $(LIB_DIR)/libdw.a
LIB_DEPS += $(LIB_DIR)/libdwfl.a
LIB_DEPS += $(LIB_DIR)/libdwelf.a
LIB_DEPS += $(LIB_DIR)/libebl.a
LIB_DEPS += $(LIB_DIR)/libelf.a
endif
# Control varialbe for address sanitizer
# Like valgrind but fast!
# You can `make clean && make jemalloc=off asan=on` to build with it.
asan = off
ifeq ($(asan),on)
CXXFLAGS += -fsanitize=address -fno-omit-frame-pointer
endif
# Control variable for allocator
# On the command line, you can `make jemalloc=off` if you definitely don't want jemalloc.
# Or you can `make jemalloc=debug` to use a version that tries to find memory errors.
jemalloc = on
ifeq ($(shell uname -s),Darwin)
jemalloc = off
endif
# Only depend on these files for the final linking stage.
# These libraries provide no headers to affect the vg build.
LINK_DEPS =
ifeq ($(jemalloc),on)
# Use jemalloc at link time
LINK_DEPS += $(LIB_DIR)/libjemalloc.a
# We have to use it statically or we can't get at its secret symbols.
LD_EXE_LIB_FLAGS += $(LIB_DIR)/libjemalloc.a
# Use the config object for jemalloc
CONFIG_OBJ += $(CONFIG_OBJ_DIR)/allocator_config_jemalloc.o
else ifeq ($(jemalloc),debug)
# Use jemalloc at link time
LINK_DEPS += $(LIB_DIR)/libjemalloc_debug.a $(LIB_DIR)/libjemalloc_debug_pic.a
# We have to use it statically or we can't get at its secret symbols.
LD_EXE_LIB_FLAGS += $(LIB_DIR)/libjemalloc_debug.a
# Use the config object for jemalloc
CONFIG_OBJ += $(CONFIG_OBJ_DIR)/allocator_config_jemalloc_debug.o
else
# Use the config object for the normal allocator
CONFIG_OBJ += $(CONFIG_OBJ_DIR)/allocator_config_system.o
endif
# common dependencies to build before all vg src files
DEPS = $(LIB_DEPS)
DEPS += $(INC_DIR)/gcsa/gcsa.h
DEPS += $(INC_DIR)/gbwt/dynamic_gbwt.h
DEPS += $(INC_DIR)/gbwtgraph/gbwtgraph.h
DEPS += $(INC_DIR)/kff_io.hpp
DEPS += $(INC_DIR)/lru_cache.h
DEPS += $(INC_DIR)/dynamic/dynamic.hpp
DEPS += $(INC_DIR)/sparsehash/sparse_hash_map
DEPS += $(INC_DIR)/sparsepp/spp.h
DEPS += $(INC_DIR)/sha1.hpp
DEPS += $(INC_DIR)/progress_bar.hpp
DEPS += $(INC_DIR)/backward.hpp
DEPS += $(INC_DIR)/dozeu/dozeu.h
DEPS += $(INC_DIR)/mmmultimap.hpp
DEPS += $(INC_DIR)/ips4o.hpp
DEPS += $(INC_DIR)/raptor2/raptor2.h
DEPS += $(INC_DIR)/BooPHF.h
DEPS += $(INC_DIR)/mio/mmap.hpp
DEPS += $(INC_DIR)/atomic_queue.h
.PHONY: clean clean-tests get-deps deps test set-path objs static static-docker docs man .pre-build version
# Aggregate all libvg deps, and exe deps other than libvg
LIBVG_DEPS = $(OBJ) $(ALGORITHMS_OBJ) $(IO_OBJ) $(DEP_OBJ) $(DEPS)
LIBVG_SHARED_DEPS = $(SHARED_OBJ) $(ALGORITHMS_SHARED_OBJ) $(IO_SHARED_OBJ) $(DEP_SHARED_OBJ) $(DEPS)
EXE_DEPS = $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIG_OBJ) $(DEPS) $(LINK_DEPS)
# We have a target we can build to do everything but link the library and executable
objs: $(LIBVG_DEPS) $(EXE_DEPS)
$(LIB_DIR)/libvg.a: $(LIBVG_DEPS)
rm -f $@
ar rs $@ $(OBJ) $(ALGORITHMS_OBJ) $(IO_OBJ) $(DEP_OBJ)
$(LIB_DIR)/libvg.$(SHARED_SUFFIX): $(LIBVG_SHARED_DEPS)
rm -f $@
$(CXX) -shared -o $@ $(SHARED_OBJ) $(ALGORITHMS_SHARED_OBJ) $(IO_SHARED_OBJ) $(DEP_SHARED_OBJ) $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LD_LIB_FLAGS) $(LD_STATIC_LIB_FLAGS) $(LD_STATIC_LIB_DEPS)
# Each test set can have its own binary, and not link everything static
$(UNITTEST_EXE): $(UNITTEST_BIN_DIR)/%: $(UNITTEST_OBJ_DIR)/%.o $(UNITTEST_SUPPORT_OBJ) $(CONFIG_OBJ) $(LIB_DIR)/libvg.$(SHARED_SUFFIX)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(UNITTEST_SUPPORT_OBJ) $(CONFIG_OBJ) $(LIB_DIR)/libvg.$(SHARED_SUFFIX) $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LD_LIB_FLAGS) $(LD_STATIC_LIB_FLAGS) $(LD_STATIC_LIB_DEPS) $(LD_EXE_LIB_FLAGS)
# For a normal dynamic build we remove the static build marker
$(BIN_DIR)/$(EXE): $(LIB_DIR)/libvg.a $(EXE_DEPS)
-rm -f $(LIB_DIR)/vg_is_static
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIG_OBJ) $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LIB_DIR)/libvg.a $(LD_LIB_FLAGS) $(START_STATIC) $(LD_STATIC_LIB_FLAGS) $(END_STATIC) $(LD_STATIC_LIB_DEPS) $(LD_EXE_LIB_FLAGS)
# We keep a file that we touch on the last static build.
# If the vg linkables are newer than the last static build, we do a build
$(LIB_DIR)/vg_is_static: $(OBJ_DIR)/main.o $(LIB_DIR)/libvg.a $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIG_OBJ) $(DEPS) $(LINK_DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$(EXE) $(OBJ_DIR)/main.o $(UNITTEST_OBJ) $(SUBCOMMAND_OBJ) $(CONFIG_OBJ) $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LIB_DIR)/libvg.a $(STATIC_FLAGS) $(LD_LIB_FLAGS) $(LD_STATIC_LIB_FLAGS) $(LD_STATIC_LIB_DEPS) $(LD_EXE_LIB_FLAGS)
-touch $(LIB_DIR)/vg_is_static
# We don't want to always rebuild the static vg if no files have changed.
# But we do need to rebuild it if files have changed.
# TODO: is there a way to query the mtimes of all the files and rebuild if they changed *or* vg isn't static?
# For now we link dynamically and then link statically, if we actually need to rebuild anything.
static: $(LIB_DIR)/vg_is_static
# Make sure to strip out the symbols that make the binary 300 MB, but leave the
# symbols perf needs for profiling.
static-docker: static scripts/*
strip -d $(BIN_DIR)/$(EXE)
DOCKER_BUILDKIT=1 docker build . -f Dockerfile.static -t vg
# We have system-level deps to install
# We want the One True Place for them to be in the Dockerfile.
get-deps:
sudo DEBIAN_FRONTEND=$(DEBIAN_FRONTEND) apt-get install -qq -y --no-upgrade $(shell cat Dockerfile | sed -n '/^###DEPS_BEGIN###/,$${p;/^###DEPS_END###/q}' | grep -v '^ *#' | grep -v "^RUN" | tr '\n' ' ' | tr -d '\\')
# And we have submodule deps to build
deps: $(DEPS)
test: $(BIN_DIR)/$(EXE) $(LIB_DIR)/libvg.a test/build_graph $(BIN_DIR)/shuf $(BIN_DIR)/vcf2tsv $(FASTAHACK_DIR)/fastahack $(BIN_DIR)/rapper
cd test && prove -v t
# Hide the compiler configuration from the doc tests, so that the ones that
# build code can't pick up libraries out of the vg build itself.
# But still supply vg on the PATH. Hope it knows where its own libraries are.
CFLAGS= CXXFLAGS= CPPFLAGS= LDFLAGS= INCLUDE_FLAGS= LIBRARY_PATH= LD_LIBRARY_PATH= DYLD_LIBRARY_PATH= DYLD_FALLBACK_LIBRARY_PATH= LD_INCLUDE_PATH= CC= CXX= CXX_STANDARD= PATH=$(CWD)/bin:$(PATH) doc/test-docs.sh
# Somebody has been polluting the test directory with temporary files that are not deleted after the tests.
# To make git status more useful, we delete everything that looks like a temporary file.
clean-test:
cd test && rm -rf tmp && mkdir tmp && mv 2_2.mat build_graph.cpp default.mat tmp && rm -f *.* && mv tmp/* . && rmdir tmp
docs: $(SRC_DIR)/*.cpp $(SRC_DIR)/*.hpp $(ALGORITHMS_SRC_DIR)/*.cpp $(ALGORITHMS_SRC_DIR)/*.hpp $(SUBCOMMAND_SRC_DIR)/*.cpp $(SUBCOMMAND_SRC_DIR)/*.hpp $(UNITTEST_SRC_DIR)/*.cpp $(UNITTEST_SRC_DIR)/*.hpp $(UNITTEST_SUPPORT_SRC_DIR)/*.cpp
doxygen
echo "View documentation at: file://$(PWD)/doc/doxygen/index.html"
man: $(patsubst doc/asciidoc/man/%.adoc,doc/man/%.1,$(wildcard doc/asciidoc/man/*.adoc))
doc/man/%.1: doc/asciidoc/man/%.adoc
asciidoctor -b manpage -d manpage -o $@ $<
# Hack to use gshuf or shuf as appropriate to the platform when testing
$(BIN_DIR)/shuf:
ifeq ($(shell uname -s),Darwin)
ln -s `which gshuf` $(BIN_DIR)/shuf
else
ln -s `which shuf` $(BIN_DIR)/shuf
endif
test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/vg.hpp
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp $(LD_LIB_DIR_FLAGS) $(LDFLAGS) $(LIB_DIR)/libvg.a $(LD_LIB_FLAGS) $(START_STATIC) $(LD_STATIC_LIB_FLAGS) $(END_STATIC) $(FILTER)
# TODO: The normal and debug jemalloc builds can't safely be run at the same time.
$(LIB_DIR)/libjemalloc.a: $(JEMALLOC_DIR)/src/*.c
+rm -f $(LIB_DIR)/libjemalloc*.* && rm -Rf $(CWD)/$(INC_DIR)/jemalloc && cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --enable-prof --disable-libdl --prefix=`pwd` $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && cp lib/libjemalloc.a $(CWD)/$(LIB_DIR)/ && cp -r include/* $(CWD)/$(INC_DIR)/
$(LIB_DIR)/libjemalloc_debug.a: $(JEMALLOC_DIR)/src/*.c
+rm -f $(LIB_DIR)/libjemalloc*.* && rm -Rf $(CWD)/$(INC_DIR)/jemalloc && cd $(JEMALLOC_DIR) && ./autogen.sh && ./configure --enable-prof --disable-libdl --enable-debug --enable-fill --prefix=`pwd` $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && cp lib/libjemalloc.a $(CWD)/$(LIB_DIR)/libjemalloc_debug.a && cp -r include/* $(CWD)/$(INC_DIR)/
# Use fake patterns to tell Make that this rule generates all these files when run once.
# Here % should always match "lib" which is a common substring.
# See https://stackoverflow.com/a/19822767
$(LIB_DIR)/%sdsl.a $(LIB_DIR)/%divsufsort.a $(LIB_DIR)/%divsufsort64.a : $(SDSL_DIR)/lib/*.cpp $(SDSL_DIR)/include/sdsl/*.hpp
ifeq ($(shell uname -s),Darwin)
+cd $(SDSL_DIR) && AS_INTEGRATED_ASSEMBLER=1 BUILD_PORTABLE=1 CXXFLAGS="-fPIC $(CPPFLAGS) $(CXXFLAGS)" ./install.sh $(CWD) $(FILTER)
else
+cd $(SDSL_DIR) && BUILD_PORTABLE=1 CXXFLAGS="-fPIC $(CPPFLAGS) $(CXXFLAGS)" ./install.sh $(CWD) $(FILTER)
endif
$(LIB_DIR)/libssw.a: $(SSW_DIR)/*.c $(SSW_DIR)/*.cpp $(SSW_DIR)/*.h
+cd $(SSW_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && ar rs $(CWD)/$(LIB_DIR)/libssw.a ssw.o ssw_cpp.o && cp ssw_cpp.h ssw.h $(CWD)/$(INC_DIR)
# We need to hide -Xpreprocessor -fopenmp from Snappy, at least on Mac, because
# it will drop the -Xpreprocessor and keep the -fopenmp and upset Clang.
$(LIB_DIR)/libsnappy.a: $(SNAPPY_DIR)/*.cc $(SNAPPY_DIR)/*.h
+cd $(SNAPPY_DIR) && ./autogen.sh && CXXFLAGS="-fPIC $(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" ./configure --prefix=$(CWD) $(FILTER) && CXXFLAGS="-fPIC $(filter-out -Xpreprocessor -fopenmp,$(CXXFLAGS))" $(MAKE) libsnappy.la $(FILTER) && cp .libs/libsnappy.a $(CWD)/lib/ && cp snappy-c.h snappy-sinksource.h snappy-stubs-public.h snappy.h $(CWD)/include/
$(INC_DIR)/gcsa/gcsa.h: $(LIB_DIR)/libgcsa2.a
$(LIB_DIR)/libgcsa2.a: $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(wildcard $(GCSA2_DIR)/*.cpp) $(wildcard $(GCSA2_DIR)/include/gcsa/*.h)
ifeq ($(shell uname -s),Darwin)
+cp -r $(GCSA2_DIR)/include/gcsa $(CWD)/$(INC_DIR)/ && cd $(GCSA2_DIR) && $(MAKE) clean && make directories && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" AS_INTEGRATED_ASSEMBLER=1 $(MAKE) lib/libgcsa2.a $(FILTER) && mv lib/libgcsa2.a $(CWD)/$(LIB_DIR)
else
+cp -r $(GCSA2_DIR)/include/gcsa $(CWD)/$(INC_DIR)/ && cd $(GCSA2_DIR) && $(MAKE) clean && make directories && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) lib/libgcsa2.a $(FILTER) && mv lib/libgcsa2.a $(CWD)/$(LIB_DIR)
endif
$(INC_DIR)/gbwt/dynamic_gbwt.h: $(LIB_DIR)/libgbwt.a
$(LIB_DIR)/libgbwt.a: $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(wildcard $(GBWT_DIR)/src/*.cpp) $(wildcard $(GBWT_DIR)/include/gbwt/*.h)
ifeq ($(shell uname -s),Darwin)
+cp -r $(GBWT_DIR)/include/gbwt $(CWD)/$(INC_DIR)/ && cd $(GBWT_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" AS_INTEGRATED_ASSEMBLER=1 $(MAKE) $(FILTER) && mv lib/libgbwt.a $(CWD)/$(LIB_DIR)
else
+cp -r $(GBWT_DIR)/include/gbwt $(CWD)/$(INC_DIR)/ && cd $(GBWT_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && mv lib/libgbwt.a $(CWD)/$(LIB_DIR)
endif
$(INC_DIR)/gbwtgraph/gbwtgraph.h: $(LIB_DIR)/libgbwtgraph.a
$(LIB_DIR)/libgbwtgraph.a: $(LIB_DIR)/libgbwt.a $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(LIB_DIR)/libhandlegraph.a $(wildcard $(GBWTGRAPH_DIR)/src/*.cpp) $(wildcard $(GBWTGRAPH_DIR)/include/gbwtgraph/*.h)
ifeq ($(shell uname -s),Darwin)
+cp -r $(GBWTGRAPH_DIR)/include/gbwtgraph $(CWD)/$(INC_DIR)/ && cd $(GBWTGRAPH_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" AS_INTEGRATED_ASSEMBLER=1 $(MAKE) $(FILTER) && mv lib/libgbwtgraph.a $(CWD)/$(LIB_DIR)
else
+cp -r $(GBWTGRAPH_DIR)/include/gbwtgraph $(CWD)/$(INC_DIR)/ && cd $(GBWTGRAPH_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && mv lib/libgbwtgraph.a $(CWD)/$(LIB_DIR)
endif
$(INC_DIR)/kff_io.hpp: $(LIB_DIR)/libkff.a
$(LIB_DIR)/libkff.a: $(KFF_DIR)/kff_io.cpp $(KFF_DIR)/kff_io.hpp.in
ifeq ($(shell uname -s),Darwin)
+cd $(KFF_DIR) && rm -Rf build && mkdir build && cd build && cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_CXX_FLAGS="-fPIC -Wall -Ofast -g $(CXXFLAGS)" .. && AS_INTEGRATED_ASSEMBLER=1 $(MAKE) $(FILTER) && cp kff_io.hpp $(CWD)/$(INC_DIR) && mv libkff.a $(CWD)/$(LIB_DIR)
else
+cd $(KFF_DIR) && rm -Rf build && mkdir build && cd build && cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_CXX_FLAGS="-fPIC -Wall -Ofast -g $(CXXFLAGS)" .. && $(MAKE) $(FILTER) && cp kff_io.hpp $(CWD)/$(INC_DIR) && mv libkff.a $(CWD)/$(LIB_DIR)
endif
$(INC_DIR)/BooPHF.h: $(BBHASH_DIR)/BooPHF.h
+cp $(BBHASH_DIR)/BooPHF.h $(CWD)/$(INC_DIR)
$(INC_DIR)/progress_bar.hpp: $(PROGRESS_BAR_DIR)/progress_bar.hpp
+cp $(PROGRESS_BAR_DIR)/progress_bar.hpp $(CWD)/$(INC_DIR)
$(OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/progress_bar.cpp $(PROGRESS_BAR_DIR)/*.hpp
+$(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $<
$(SHARED_OBJ_DIR)/progress_bar.o: $(PROGRESS_BAR_DIR)/progress_bar.cpp $(PROGRESS_BAR_DIR)/*.hpp
+$(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $<
$(INC_DIR)/Fasta.h: $(FASTAHACK_DIR)/Fasta.h
+cd $(FASTAHACK_DIR) && cp Fasta.h $(CWD)/$(INC_DIR)
$(OBJ_DIR)/Fasta.o: $(FASTAHACK_DIR)/Fasta.cpp $(INC_DIR)/Fasta.h
+$(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $< $(FILTER)
$(SHARED_OBJ_DIR)/Fasta.o: $(FASTAHACK_DIR)/Fasta.cpp $(INC_DIR)/Fasta.h
+$(CXX) -I$(FASTAHACK_DIR) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< $(FILTER)
# We have this target to clean up the old Protobuf we used to have.
# We can remove it after we no longer care about building properly on a dirty
# build from vg versions that shipped Protobuf themselves.
$(LIB_DIR)/cleaned_old_protobuf_v003: $(wildcard $(LIB_DIR)/libproto*) $(wildcard $(LIB_DIR)/pkgconfig/protobuf*)
+rm -f $(LIB_DIR)/cleaned_old_protobuf*
+rm -f $(LIB_DIR)/libproto* $(LIB_DIR)/pkgconfig/protobuf* $(BIN_DIR)/protoc
+rm -Rf $(INC_DIR)/google/protobuf deps/protobuf
+touch $(LIB_DIR)/cleaned_old_protobuf_v003
# We used to ship our own version of boost, but now we use the system version instead.
$(LIB_DIR)/cleaned_old_boost: $(wildcard $(LIB_DIR)/libboost_*) $(wildcard $(INC_DIR)/boost/*)
+rm -f $(LIB_DIR)/libboost_*
+rm -Rf $(INC_DIR)/boost
+touch $(LIB_DIR)/cleaned_old_boost
# We used to build elfutils with libdebuginfod, but we now need to build
# without it.
$(LIB_DIR)/cleaned_old_elfutils:
+rm -f $(LIB_DIR)/libelf.a $(LIB_DIR)/libebl.a $(LIB_DIR)/libdwfl.a $(LIB_DIR)/libdwelf.a $(LIB_DIR)/libdw.a
+touch $(LIB_DIR)/cleaned_old_elfutils
$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/libhandlegraph.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIB_DIR)/cleaned_old_protobuf_v003 $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp $(LIBVGIO_DIR)/deps/vg.proto
+rm -f $(CWD)/$(INC_DIR)/vg.pb.h $(CWD)/$(INC_DIR)/vg/vg.pb.h
+rm -Rf $(CWD)/$(INC_DIR)/vg/io/
+export CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" && export LDFLAGS="$(LD_LIB_DIR_FLAGS) $(LDFLAGS)" && cd $(LIBVGIO_DIR) && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && rm -rf build-vg && mkdir build-vg && cd build-vg && PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_CXX_STANDARD=$(CXX_STANDARD) -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib .. $(FILTER) && $(MAKE) clean && VERBOSE=1 $(MAKE) $(FILTER) && $(MAKE) install
$(LIB_DIR)/libhandlegraph.a: $(LIBHANDLEGRAPH_DIR)/src/include/handlegraph/*.hpp $(LIBHANDLEGRAPH_DIR)/src/*.cpp
+cd $(LIBHANDLEGRAPH_DIR) && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="$(CXXFLAGS) $(CPPFLAGS)" cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib .. && $(MAKE) $(FILTER) && $(MAKE) install
# On Linux, libdeflate builds a .so.
# On Mac, it *still* builds an so, which is just a dylib with .so extension.
# On Mac we need to make sure to set the install name. We do that by renaming to dylib.
# We don't just leave it as .so because we need to deal with outdated .so files with no paths set.
$(LIB_DIR)/libdeflate.$(SHARED_SUFFIX): $(LIB_DIR)/libdeflate.a
+cd $(LIBDEFLATE_DIR) && cp libdeflate.so $(CWD)/$(LIB_DIR)
+touch $(CWD)/$(LIB_DIR)/libdeflate.so
ifeq ($(shell uname -s),Darwin)
+mv $(LIB_DIR)/libdeflate.so $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX)
+install_name_tool -id $(CWD)/$(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX)
endif
$(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DIR)/*.h $(LIBDEFLATE_DIR)/lib/*.h $(LIBDEFLATE_DIR)/lib/*/*.h $(LIBDEFLATE_DIR)/lib/*.c $(LIBDEFLATE_DIR)/lib/*/*.c
+cd $(LIBDEFLATE_DIR) && V=1 LDFLAGS="$(LDFLAGS) $(LD_RENAMEABLE_FLAGS)" $(MAKE) $(FILTER) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)
# We build htslib after libdeflate so it can use libdeflate.
# We need to do some wizardry to get it to pick up the right build and target system types on modern autotools.
# We have to do a full build in order to install, to get the pkg-config file so libvgio can link against it.
# We also have to have the shared libdeflate or we will get complaints that the static one is not position independent.
# If we need either the library or the pkg-config file (which we didn't used to ship), run the whole build.
# We use a wildcard match to make sure make understands that both files come from one command run.
# See https://stackoverflow.com/a/3077254
# We also need to make sure that htslib searches itself before system paths, as
# a system path, in case another htslib is installed on the system. Some HTSlib
# headers look for the current HTSlib with <>.
$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc $(LIB_DIR)/libhts%$(SHARED_SUFFIX): $(LIB_DIR)/libdeflate.a $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
+cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoreconf -i && autoheader && autoconf || true
+cd $(HTSLIB_DIR) && (./configure -n 2>&1 || true) | grep "build system type" | rev | cut -f1 -d' ' | rev >systype.txt
+cd $(HTSLIB_DIR) && CFLAGS="-I$(CWD)/$(HTSLIB_DIR) -isystem $(CWD)/$(HTSLIB_DIR) -I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="$(LDFLAGS) -L$(CWD)/$(LIB_DIR) $(LD_UTIL_RPATH_FLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) --host=$$(cat systype.txt) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
# Build and install tabixpp for vcflib.
$(LIB_DIR)/libtabixpp.a: $(LIB_DIR)/libhts.a $(TABIXPP_DIR)/*.cpp $(TABIXPP_DIR)/*.hpp
+cd $(TABIXPP_DIR) && rm -f tabix.o libtabixpp.a && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" INCLUDES="-I$(CWD)/$(INC_DIR)" HTS_HEADERS="" $(MAKE) tabix.o $(FILTER) && ar rcs libtabixpp.a tabix.o
+cp $(TABIXPP_DIR)/libtabixpp.a $(LIB_DIR) && cp $(TABIXPP_DIR)/tabix.hpp $(INC_DIR)
+echo "Name: tabixpp" > $(LIB_DIR)/pkgconfig/tabixpp.pc
+echo "Description: Self-packaged tabixpp" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
+echo "Version: 1.0" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
+echo "Cflags: -I$(CWD)/$(INC_DIR)" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
+echo "Libs: -L$(CWD)/$(LIB_DIR) -ltabixpp" >> $(LIB_DIR)/pkgconfig/tabixpp.pc
# Build vcflib. Install the library and headers but not binaries or man pages.
# We need to build as RelWithDebInfo to avoid vcflib using its own
# -march=native, which would conflict with the -march that comes in through
# CXXFLAGS from the vg Dockerfile.
# We also need to use the magic path hint to let CMake find Mac OpenMP.
# We need to use /usr first for CMake search or Ubuntu 22.04 will decide pybind11 is installed in / when actually it is only fully installed in /usr.
$(LIB_DIR)/libvcflib.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/libtabixpp.a $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.hpp $(VCFLIB_DIR)/contrib/*/*.cpp $(VCFLIB_DIR)/contrib/*/*.h
+rm -f $(VCFLIB_DIR)/contrib/WFA2-lib/VERSION
+cd $(VCFLIB_DIR) && rm -Rf build && mkdir build && cd build && PKG_CONFIG_PATH="$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH)" cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DZIG=OFF -DCMAKE_C_FLAGS="$(CFLAGS)" -DCMAKE_CXX_FLAGS="$(CXXFLAGS) ${CPPFLAGS}" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_PREFIX_PATH="/usr;$(OMP_PREFIXES)" .. && cmake --build .
+cp $(VCFLIB_DIR)/contrib/filevercmp/*.h* $(INC_DIR)
+cp $(VCFLIB_DIR)/contrib/fastahack/*.h* $(INC_DIR)
+cp $(VCFLIB_DIR)/contrib/smithwaterman/*.h* $(INC_DIR)
+cp $(VCFLIB_DIR)/contrib/intervaltree/*.h* $(INC_DIR)
+cp $(VCFLIB_DIR)/contrib/multichoose/*.h* $(INC_DIR)
+cp $(VCFLIB_DIR)/src/*.h* $(INC_DIR)
+cp $(VCFLIB_DIR)/build/libvcflib.a $(LIB_DIR)
# vcflib binaries are all automatically built. We need this one.
$(BIN_DIR)/vcf2tsv: $(VCFLIB_DIR)/src/*.cpp $(VCFLIB_DIR)/src/*.h $(LIB_DIR)/libvcflib.a
+cp $(VCFLIB_DIR)/build/vcf2tsv $(BIN_DIR)
$(FASTAHACK_DIR)/fastahack: $(FASTAHACK_DIR)/*.c $(FASTAHACK_DIR)/*.h $(FASTAHACK_DIR)/*.cpp
+cd $(FASTAHACK_DIR) && $(MAKE) $(FILTER)
$(LIB_DIR)/libgssw.a: $(GSSW_DIR)/src/gssw.c $(GSSW_DIR)/src/gssw.h
+cd $(GSSW_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp lib/libgssw.a $(CWD)/$(LIB_DIR)/ && cp src/gssw.h $(CWD)/$(INC_DIR)/
$(INC_DIR)/lru_cache.h: $(DEP_DIR)/lru_cache/*.h $(DEP_DIR)/lru_cache/*.cc
+cd $(DEP_DIR)/lru_cache && cp *.h* $(CWD)/$(INC_DIR)/
# We moved the Dynamic headers so make sure to clean up the old ones.
$(INC_DIR)/dynamic/dynamic.hpp: $(DYNAMIC_DIR)/include/dynamic/*.hpp $(DYNAMIC_DIR)/include/dynamic/*/*.hpp
+rm -Rf $(INC_DIR)/dynamic.hpp $(INC_DIR)/dynamic
# annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers
+cd $(CWD)/$(DYNAMIC_DIR) && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="$(CPPFLAGS) $(CXXFLAGS)" && cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" -DCMAKE_VERBOSE_MAKEFILE=ON .. && make && cp -r $(CWD)/$(DYNAMIC_DIR)/deps/hopscotch_map/include/* $(CWD)/$(INC_DIR)/
# Do the copy of the main file last so we can tell if this recipe failed and redo it.
# Otherwise we get dynamic.hpp without its deps
+mkdir -p $(INC_DIR)/dynamic && cp -r $(CWD)/$(DYNAMIC_DIR)/include/dynamic/* $(INC_DIR)/dynamic/
$(INC_DIR)/sparsehash/sparse_hash_map: $(wildcard $(SPARSEHASH_DIR)/**/*.cc) $(wildcard $(SPARSEHASH_DIR)/**/*.h)
+cd $(SPARSEHASH_DIR) && ./autogen.sh && LDFLAGS="$(LD_LIB_DIR_FLAGS) $(LDFLAGS)" ./configure --prefix=$(CWD) $(FILTER) && $(MAKE) $(FILTER) && $(MAKE) install
$(INC_DIR)/sparsepp/spp.h: $(wildcard $(SPARSEHASH_DIR)/sparsepp/*.h)
+cp -r $(SPARSEPP_DIR)/sparsepp $(INC_DIR)/
#$(INC_DIR)/Variant.h
$(LIB_DIR)/libvcfh.a: $(DEP_DIR)/libVCFH/*.cpp $(DEP_DIR)/libVCFH/*.hpp
+cd $(DEP_DIR)/libVCFH && $(MAKE) $(FILTER) && cp libvcfh.a $(CWD)/$(LIB_DIR)/ && cp vcfheader.hpp $(CWD)/$(INC_DIR)/
$(LIB_DIR)/libsonlib.a: $(CWD)/$(DEP_DIR)/sonLib/C/inc/*.h $(CWD)/$(DEP_DIR)/sonLib/C/impl/*.c
+cd $(DEP_DIR)/sonLib && $(MAKE) clean && kyotoTycoonLib="" CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp lib/sonLib.a $(CWD)/$(LIB_DIR)/libsonlib.a && mkdir -p $(CWD)/$(INC_DIR)/sonLib && cp lib/*.h $(CWD)/$(INC_DIR)/sonLib
$(LIB_DIR)/libpinchesandcacti.a: $(LIB_DIR)/libsonlib.a $(CWD)/$(DEP_DIR)/pinchesAndCacti/inc/*.h $(CWD)/$(DEP_DIR)/pinchesAndCacti/impl/*.c
+cd $(DEP_DIR)/pinchesAndCacti && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cd $(CWD)/$(DEP_DIR)/sonLib && cp lib/stPinchesAndCacti.a $(CWD)/$(LIB_DIR)/libpinchesandcacti.a && cp lib/3EdgeConnected.a $(CWD)/$(LIB_DIR)/lib3edgeconnected.a && mkdir -p $(CWD)/$(INC_DIR)/sonLib && cp lib/*.h $(CWD)/$(INC_DIR)/sonLib
# When building raptor we need to make sure to pre-generate and fix up the lexer
# We also need to clear out its cmake stuff in case it found a wrong Bison and cached it.
$(LIB_DIR)/libraptor2.a: $(RAPTOR_DIR)/src/* $(wildcard $(RAPTOR_DIR)/build/*)
which bison
+cd $(RAPTOR_DIR)/build && rm -Rf CMakeCache.txt CMakeFiles CTestTestfile.cmake Makefile cmake_install.cmake src tests utils && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" cmake -DCMAKE_C_COMPILER="$(CC)" -DCMAKE_CXX_COMPILER="$(CXX)" .. && rm -f src/turtle_parser.c && rm -f src/turtle_lexer.c && make turtle_lexer_tgt && make -f src/CMakeFiles/raptor2.dir/build.make src/turtle_lexer.c && sed -i.bak '/yycleanup/d' src/turtle_lexer.c && $(MAKE) $(FILTER) && cp src/libraptor2.a $(CWD)/$(LIB_DIR)
+touch $(LIB_DIR)/libraptor2.a
# We need rapper from Raptor for the tests
$(BIN_DIR)/rapper: $(LIB_DIR)/libraptor2.a
+cp $(RAPTOR_DIR)/build/utils/rapper $(BIN_DIR)/
# The Raptor header needs to be newer than the library.
# Mac Travis managed to get an old header with a new binary.
$(INC_DIR)/raptor2/raptor2.h: $(LIB_DIR)/libraptor2.a $(RAPTOR_DIR)/build/*
+cd $(RAPTOR_DIR)/build && mkdir -p $(CWD)/$(INC_DIR)/raptor2 && cp src/*.h $(CWD)/$(INC_DIR)/raptor2
+touch $(INC_DIR)/raptor2/raptor2.h
$(LIB_DIR)/libstructures.a: $(STRUCTURES_DIR)/src/include/structures/*.hpp $(STRUCTURES_DIR)/src/*.cpp $(STRUCTURES_DIR)/Makefile
+cd $(STRUCTURES_DIR) && $(MAKE) clean && $(MAKE) lib/libstructures.a $(FILTER) && cp lib/libstructures.a $(CWD)/$(LIB_DIR)/ && cp -r src/include/structures $(CWD)/$(INC_DIR)/
$(INC_DIR)/sha1.hpp: $(SHA1_DIR)/sha1.hpp
+cp $(SHA1_DIR)/*.h* $(CWD)/$(INC_DIR)/
$(INC_DIR)/backward.hpp: $(BACKWARD_CPP_DIR)/backward.hpp
+cp $(BACKWARD_CPP_DIR)/backward.hpp $(CWD)/$(INC_DIR)/
$(INC_DIR)/simde/x86/sse4.1.h: $(DOZEU_DIR)/simde/*.h $(DOZEU_DIR)/simde/x86/*.h
+cp -r $(DOZEU_DIR)/simde $(INC_DIR)
$(INC_DIR)/dozeu/dozeu.h: $(DOZEU_DIR)/*.h $(INC_DIR)/simde/x86/sse4.1.h
+mkdir -p $(CWD)/$(INC_DIR)/dozeu && cp $(DOZEU_DIR)/*.h $(CWD)/$(INC_DIR)/dozeu/
$(LIB_DIR)/libebl.a: $(LIB_DIR)/libelf.a
$(LIB_DIR)/libdw.a: $(LIB_DIR)/libelf.a
$(LIB_DIR)/libdwelf.a: $(LIB_DIR)/libelf.a
$(LIB_DIR)/libdwfl.a: $(LIB_DIR)/libelf.a
# We can't build elfutils from Git without "maintainer mode".
# There are some release-only headers or something that it complains it can't find otherwise.
# We also don't do a normal make and make install here because we don't want to build and install all the elfutils binaries and libasm.
# We need to disable libdebuginfod or the static binary will try and load it at
# runtime and pull in incompatible libs it depends on on whatever system it's
# running on.
$(LIB_DIR)/libelf.a: $(ELFUTILS_DIR)/libebl/*.c $(ELFUTILS_DIR)/libebl/*.h $(ELFUTILS_DIR)/libdw/*.c $(ELFUTILS_DIR)/libdw/*.h $(ELFUTILS_DIR)/libelf/*.c $(ELFUTILS_DIR)/libelf/*.h $(ELFUTILS_DIR)/src/*.c $(ELFUTILS_DIR)/src/*.h $(LIB_DIR)/cleaned_old_elfutils
+cd $(CWD)/$(INC_DIR)/ && rm -Rf elfutils gelf.h libelf.h dwarf.h libdwflP.h libdwfl.h libebl.h libelf.h
+cd $(ELFUTILS_DIR) && autoreconf -i -f && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" ./configure --enable-maintainer-mode --disable-libdebuginfod --disable-debuginfod --prefix=$(CWD) $(FILTER)
+cd $(ELFUTILS_DIR)/libelf && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libelf.a $(FILTER)
+cd $(ELFUTILS_DIR)/libebl && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libebl.a $(FILTER)
+cd $(ELFUTILS_DIR)/libdwfl && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libdwfl.a $(FILTER)
+cd $(ELFUTILS_DIR)/libdwelf && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libdwelf.a $(FILTER)
+cd $(ELFUTILS_DIR)/lib && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libeu.a $(FILTER)
+cd $(ELFUTILS_DIR)/libcpu && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) libcpu.a $(FILTER)
+cd $(ELFUTILS_DIR)/backends && $(MAKE) clean CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" && $(MAKE) libebl_backends.a $(FILTER)
+cd $(ELFUTILS_DIR)/libdw && $(MAKE) clean CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" && $(MAKE) libdw.a known-dwarf.h $(FILTER)
+cd $(ELFUTILS_DIR) && mkdir -p $(CWD)/$(INC_DIR)/elfutils && cp libdw/known-dwarf.h libdw/libdw.h libebl/libebl.h libelf/elf-knowledge.h version.h libdwfl/libdwfl.h libdwelf/libdwelf.h $(CWD)/$(INC_DIR)/elfutils && cp libelf/gelf.h libelf/libelf.h libdw/dwarf.h $(CWD)/$(INC_DIR) && cp libebl/libebl.a libdw/libdw.a libdwfl/libdwfl.a libdwelf/libdwelf.a libelf/libelf.a $(CWD)/$(LIB_DIR)/
$(OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -c -o $@ $< $(FILTER)
$(SHARED_OBJ_DIR)/sha1.o: $(SHA1_DIR)/sha1.cpp $(SHA1_DIR)/sha1.hpp
+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< $(FILTER)
$(LIB_DIR)/libfml.a: $(FERMI_DIR)/*.h $(FERMI_DIR)/*.c
cd $(FERMI_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(CFLAGS)" CXXFLAGS="-fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp *.h $(CWD)/$(INC_DIR)/ && cp libfml.a $(CWD)/$(LIB_DIR)/
# We don't need to hack the build to point at our htslib because sublinearLS gets its htslib from the include flags we set
# But we do need to hack out the return type error to work around https://github.com/yoheirosen/sublinear-Li-Stephens/issues/6
# TODO: This probably means actually calling some things in the library is unsafe!
$(LIB_DIR)/libsublinearLS.a: $(LINLS_DIR)/src/*.cpp $(LINLS_DIR)/src/*.hpp $(LIB_DIR)/libhts.a
cd $(LINLS_DIR) && $(MAKE) clean && CFLAGS="-fPIC $(filter-out -Werror=return-type,$(CFLAGS))" CXXFLAGS="-fPIC $(filter-out -Werror=return-type,$(CXXFLAGS))" INCLUDE_FLAGS="-I$(CWD)/$(INC_DIR)" $(MAKE) libs $(FILTER) && cp lib/libsublinearLS.a $(CWD)/$(LIB_DIR)/ && mkdir -p $(CWD)/$(INC_DIR)/sublinearLS && cp src/*.hpp $(CWD)/$(INC_DIR)/sublinearLS/
$(LIB_DIR)/libbdsg.a: $(INC_DIR)/BooPHF.h $(LIBBDSG_DIR)/Makefile $(LIBBDSG_DIR)/bdsg/src/*.cpp $(LIBBDSG_DIR)/bdsg/include/bdsg/*.hpp $(LIBBDSG_DIR)/bdsg/include/bdsg/internal/*.hpp $(LIBBDSG_DIR)/bdsg/include/bdsg/overlays/*.hpp $(LIB_DIR)/libhandlegraph.a $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(INC_DIR)/sparsepp/spp.h $(INC_DIR)/dynamic/dynamic.hpp $(INC_DIR)/mio/mmap.hpp
+rm -Rf $(CWD)/$(INC_DIR)/bdsg && cd $(LIBBDSG_DIR) && $(MAKE) clean && CPLUS_INCLUDE_PATH=$(CWD)/$(INC_DIR):$(CWD)/$(INC_DIR)/dynamic:$(CPLUS_INCLUDE_PATH) CXXFLAGS="$(INCLUDE_FLAGS) -fPIC $(CXXFLAGS)" $(MAKE) $(FILTER) && cp lib/libbdsg.a $(CWD)/$(LIB_DIR) && cp -r bdsg/include/* $(CWD)/$(INC_DIR)
$(INC_DIR)/mio/mmap.hpp: $(MIO_DIR)/include/mio/*
+cp -r $(MIO_DIR)/include/mio $(CWD)/$(INC_DIR)/
# It would be better to copy the atomic_queue directory rather than its contents, but to avoid re-writing mmmultimap...
$(INC_DIR)/atomic_queue.h: $(ATOMIC_QUEUE_DIR)/include/*
+cp -r $(ATOMIC_QUEUE_DIR)/include/atomic_queue/* $(CWD)/$(INC_DIR)/
$(INC_DIR)/mmmultiset.hpp: $(MMMULTIMAP_DIR)/src/mmmultiset.hpp $(INC_DIR)/mmmultimap.hpp
$(INC_DIR)/mmmultimap.hpp: $(MMMULTIMAP_DIR)/src/mmmultimap.hpp $(MMMULTIMAP_DIR)/src/mmmultiset.hpp $(INC_DIR)/mio/mmap.hpp $(INC_DIR)/atomic_queue.h
+cp $(MMMULTIMAP_DIR)/src/mmmultimap.hpp $(MMMULTIMAP_DIR)/src/mmmultiset.hpp $(CWD)/$(INC_DIR)/
$(INC_DIR)/ips4o.hpp: $(IPS4O_DIR)/ips4o.hpp $(IPS4O_DIR)/ips4o/*
+cp -r $(IPS4O_DIR)/ips4o* $(CWD)/$(INC_DIR)/
# The xg repo has a cmake build system based all around external projects, and
# we need it to use our installed versions of everything instead.
# We also need to not build against GFAKluge
$(LIB_DIR)/libxg.a: $(XG_DIR)/src/*.hpp $(XG_DIR)/src/*.cpp $(INC_DIR)/mmmultimap.hpp $(INC_DIR)/ips4o.hpp $(LIB_DIR)/libhandlegraph.a $(LIB_DIR)/libsdsl.a $(LIB_DIR)/libdivsufsort.a $(LIB_DIR)/libdivsufsort64.a $(INC_DIR)/mio/mmap.hpp $(INC_DIR)/atomic_queue.h
+rm -f $@
+cp -r $(XG_DIR)/src/*.hpp $(CWD)/$(INC_DIR)
+$(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) $(CPPFLAGS) -fPIC -DNO_GFAKLUGE -c -o $(XG_DIR)/xg.o $(XG_DIR)/src/xg.cpp $(FILTER)
+ar rs $@ $(XG_DIR)/xg.o
# Auto-git-versioning
# Can be overridden from the environment to supply a version if none is on disk.
VG_GIT_VERSION ?= unknown
# Clean old path
$(shell rm -f $(INC_DIR)/vg_git_version.hpp)
# Decide if .git exists and needs to be watched
ifeq ($(shell if [ -d .git ]; then echo present; else echo absent; fi),present)
# If so, try and make a git version file.
# We used to do this by having a phony target to depend on, but Make won't
# detect that the phony target is altering a different file, so it would
# take 2 make runs to pick up the right version.
# Build a real git version file.
# If it's not the same as the old one, replace the old one.
# If it is the same, do nothing and don't rebuild dependent targets.
$(info Check Git)
$(shell echo "#define VG_GIT_VERSION \"$(shell git describe --always --tags 2>/dev/null || echo git-error)\"" > $(SRC_DIR)/vg_git_version.hpp.tmp)
$(shell diff $(SRC_DIR)/vg_git_version.hpp.tmp $(SRC_DIR)/vg_git_version.hpp >/dev/null 2>/dev/null || cp $(SRC_DIR)/vg_git_version.hpp.tmp $(SRC_DIR)/vg_git_version.hpp)
$(shell rm -f $(SRC_DIR)/vg_git_version.hpp.tmp)
else
# Just use the version file we have, if any.
$(info Do not check Git)
$(shell if [ ! -e $(SRC_DIR)/vg_git_version.hpp] ; then echo "#define VG_GIT_VERSION \"$(VG_GIT_VERSION)\"" > $(SRC_DIR)/vg_git_version.hpp ; fi)
endif
# We have a do-nothing target so we can "make version"
version:
@echo "Version information up to date"
# Build an environment version file.
# If it's not the same as the old one, replace the old one.
# If it is the same, do nothing and don't rebuild dependent targets.
# Clean old path
$(shell rm -f $(INC_DIR)/vg_environment_version.hpp)
$(shell echo "#define VG_COMPILER_VERSION \"$(shell $(CXX) --version 2>/dev/null | head -n 1)\"" > $(SRC_DIR)/vg_environment_version.hpp.tmp)
$(shell echo "#define VG_OS \"$(shell uname)\"" >> $(SRC_DIR)/vg_environment_version.hpp.tmp)
$(shell echo "#define VG_BUILD_USER \"$(shell whoami)\"" >> $(SRC_DIR)/vg_environment_version.hpp.tmp)
$(shell echo "#define VG_BUILD_HOST \"$(shell hostname)\"" >> $(SRC_DIR)/vg_environment_version.hpp.tmp)
$(shell diff $(SRC_DIR)/vg_environment_version.hpp.tmp $(SRC_DIR)/vg_environment_version.hpp >/dev/null 2>/dev/null || cp $(SRC_DIR)/vg_environment_version.hpp.tmp $(SRC_DIR)/vg_environment_version.hpp)
$(shell rm -f $(SRC_DIR)/vg_environment_version.hpp.tmp)
###################################
## VG source code compilation begins here
####################################
$(OBJ_DIR)/version.o: $(SRC_DIR)/version.cpp $(SRC_DIR)/version.hpp $(SRC_DIR)/vg_git_version.hpp $(SRC_DIR)/vg_environment_version.hpp
########################
## Pattern Rules
########################
# Define a default rule for building objects from CPP files
# Depend on the .d file so we rebuild if dependency info is missing/deleted
# Make sure to touch the .o file after the compiler finishes so it is always newer than the .d file
# Use static pattern rules so the dependency files will not be ignored if the output exists
# See <https://stackoverflow.com/a/34983297>
$(OBJ) $(OBJ_DIR)/main.o: $(OBJ_DIR)/%.o : $(SRC_DIR)/%.cpp $(OBJ_DIR)/%.d $(DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
$(SHARED_OBJ): $(SHARED_OBJ_DIR)/%.o : $(SRC_DIR)/%.cpp $(SHARED_OBJ_DIR)/%.d $(DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
@touch $@
$(ALGORITHMS_OBJ): $(ALGORITHMS_OBJ_DIR)/%.o : $(ALGORITHMS_SRC_DIR)/%.cpp $(ALGORITHMS_OBJ_DIR)/%.d $(DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
$(ALGORITHMS_SHARED_OBJ): $(ALGORITHMS_SHARED_OBJ_DIR)/%.o : $(ALGORITHMS_SRC_DIR)/%.cpp $(ALGORITHMS_SHARED_OBJ_DIR)/%.d $(DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
@touch $@
$(IO_OBJ): $(IO_OBJ_DIR)/%.o : $(IO_SRC_DIR)/%.cpp $(IO_OBJ_DIR)/%.d $(DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
$(IO_SHARED_OBJ): $(IO_SHARED_OBJ_DIR)/%.o : $(IO_SRC_DIR)/%.cpp $(IO_SHARED_OBJ_DIR)/%.d $(DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -fPIC -c -o $@ $< $(FILTER)
@touch $@
$(SUBCOMMAND_OBJ): $(SUBCOMMAND_OBJ_DIR)/%.o : $(SUBCOMMAND_SRC_DIR)/%.cpp $(SUBCOMMAND_OBJ_DIR)/%.d $(DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
$(UNITTEST_OBJ): $(UNITTEST_OBJ_DIR)/%.o : $(UNITTEST_SRC_DIR)/%.cpp $(UNITTEST_OBJ_DIR)/%.d $(DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
$(UNITTEST_SUPPORT_OBJ): $(UNITTEST_SUPPORT_OBJ_DIR)/%.o : $(UNITTEST_SUPPORT_SRC_DIR)/%.cpp $(UNITTEST_SUPPORT_OBJ_DIR)/%.d $(DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
# Config objects get individual rules
$(CONFIG_OBJ_DIR)/allocator_config_jemalloc.o: $(CONFIG_SRC_DIR)/allocator_config_jemalloc.cpp $(CONFIG_OBJ_DIR)/allocator_config_jemalloc.d $(DEPS) $(LIB_DIR)/libjemalloc.a
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
$(CONFIG_OBJ_DIR)/allocator_config_jemalloc_debug.o: $(CONFIG_SRC_DIR)/allocator_config_jemalloc_debug.cpp $(CONFIG_OBJ_DIR)/allocator_config_jemalloc_debug.d $(DEPS) $(LIB_DIR)/libjemalloc_debug.a
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
$(CONFIG_OBJ_DIR)/allocator_config_system.o: $(CONFIG_SRC_DIR)/allocator_config_system.cpp $(CONFIG_OBJ_DIR)/allocator_config_system.d $(DEPS)
$(CXX) $(INCLUDE_FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(DEPGEN_FLAGS) -c -o $@ $< $(FILTER)
@touch $@
# Use a fake rule to build .d files, so we don't complain if they don't exist.
$(OBJ_DIR)/%.d: ;
$(ALGORITHMS_OBJ_DIR)/%.d: ;
$(CONFIG_OBJ_DIR)/%.d: ;
$(IO_OBJ_DIR)/%.d: ;
$(SUBCOMMAND_OBJ_DIR)/%.d: ;
$(UNITTEST_OBJ_DIR)/%.d: ;
# Don't delete them.
.PRECIOUS: $(OBJ_DIR)/%.d $(ALGORITHMS_OBJ_DIR)/%.d $(CONFIG_OBJ_DIR)/%.d $(IO_OBJ_DIR)/%.d $(SUBCOMMAND_OBJ_DIR)/%.d $(UNITTEST_OBJ_DIR)/%.d
# Use no implicit rules
.SUFFIXES:
###################################
## VG source code compilation ends here
####################################
# Make directories before quitting target due to missing protoc.
# If we run the rest of the build without these, lib and include can become files.
# TODO: quitting if no protoc doesn't reliably stop the build.
.pre-build:
@if [ ! -d $(BIN_DIR) ]; then mkdir -p $(BIN_DIR); fi
@if [ ! -d $(UNITTEST_BIN_DIR) ]; then mkdir -p $(UNITTEST_BIN_DIR); fi
@if [ ! -d $(LIB_DIR) ]; then mkdir -p $(LIB_DIR); fi
@if [ ! -d $(OBJ_DIR) ]; then mkdir -p $(OBJ_DIR); fi
@if [ ! -d $(SHARED_OBJ_DIR) ]; then mkdir -p $(SHARED_OBJ_DIR); fi
@if [ ! -d $(ALGORITHMS_OBJ_DIR) ]; then mkdir -p $(ALGORITHMS_OBJ_DIR); fi
@if [ ! -d $(ALGORITHMS_SHARED_OBJ_DIR) ]; then mkdir -p $(ALGORITHMS_SHARED_OBJ_DIR); fi
@if [ ! -d $(CONFIG_OBJ_DIR) ]; then mkdir -p $(CONFIG_OBJ_DIR); fi
@if [ ! -d $(IO_OBJ_DIR) ]; then mkdir -p $(IO_OBJ_DIR); fi
@if [ ! -d $(IO_SHARED_OBJ_DIR) ]; then mkdir -p $(IO_SHARED_OBJ_DIR); fi
@if [ ! -d $(SUBCOMMAND_OBJ_DIR) ]; then mkdir -p $(SUBCOMMAND_OBJ_DIR); fi
@if [ ! -d $(UNITTEST_OBJ_DIR) ]; then mkdir -p $(UNITTEST_OBJ_DIR); fi
@if [ ! -d $(UNITTEST_SUPPORT_OBJ_DIR) ]; then mkdir -p $(UNITTEST_SUPPORT_OBJ_DIR); fi
@if [ ! -d $(INC_DIR) ]; then mkdir -p $(INC_DIR); fi