mirror of
https://github.com/lh3/minimap2.git
synced 2026-09-15 21:17:54 +08:00
201 lines
6.5 KiB
Makefile
201 lines
6.5 KiB
Makefile
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## /* The MIT License
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##
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## Copyright (c) 2018- Dana-Farber Cancer Institute
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## 2017-2018 Broad Institute, Inc.
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##
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## Permission is hereby granted, free of charge, to any person obtaining
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## a copy of this software and associated documentation files (the
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## "Software"), to deal in the Software without restriction, including
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## without limitation the rights to use, copy, modify, merge, publish,
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## distribute, sublicense, and/or sell copies of the Software, and to
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## permit persons to whom the Software is furnished to do so, subject to
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## the following conditions:
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##
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## The above copyright notice and this permission notice shall be
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## included in all copies or substantial portions of the Software.
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##
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## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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## EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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## MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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## NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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## BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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## ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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## CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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## SOFTWARE.
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## Modified Copyright (C) 2021 Intel Corporation
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## Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>;
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## Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
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## Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
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## */
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##
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CFLAGS= -Wall -O2 -Wc++-compat #-Wextra
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CPPFLAGS= -DHAVE_KALLOC -march=native
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OPT_FLAGS= -DVECTORIZED_CHAINING -DALIGN_AVX
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ifeq ($(lhash), 1)
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OPT_FLAGS+= -DLISA_HASH -DUINT64 -DVECTORIZE
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endif
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ifeq ($(manual_profile), 1)
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CPPFLAGS+= -DMANUAL_PROFILING
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endif
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ifeq ($(arch), avx512)
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CPPFLAGS+= -xCORE-AVX512
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endif
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ifeq ($(disable_output), 1)
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CPPFLAGS+= -DDISABLE_OUTPUT
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endif
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ifeq ($(no_opt),)
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CPPFLAGS+= $(OPT_FLAGS)
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endif
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INCLUDES= -I./ext/TAL/src/LISA-hash -I./ext/TAL/src/dynamic-programming
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OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o
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PROG= minimap2
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PROG_EXTRA= sdust minimap2-lite
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LIBS= -lm -lz -lpthread
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CC=$(CXX)
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ifeq ($(CC), g++)
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CC=g++ -std=c++11
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endif
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ifeq ($(arm_neon),) # if arm_neon is not defined
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ifeq ($(sse2only),) # if sse2only is not defined
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OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o ksw2_extd2_avx.o
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else # if sse2only is defined
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OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
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endif
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else # if arm_neon is defined
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OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
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INCLUDES+=-Isse2neon
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ifeq ($(aarch64),) #if aarch64 is not defined
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CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
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else #if aarch64 is defined
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CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
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endif
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endif
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ifneq ($(asan),)
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CFLAGS+=-fsanitize=address
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LIBS+=-fsanitize=address
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endif
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ifneq ($(tsan),)
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CFLAGS+=-fsanitize=thread
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LIBS+=-fsanitize=thread
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endif
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.PHONY:all extra clean depend
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.SUFFIXES:.c .o
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.c.o:
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$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
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all:$(PROG)
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extra:all $(PROG_EXTRA)
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minimap2:main.o libminimap2.a
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$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
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minimap2-lite:example.o libminimap2.a
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$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
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libminimap2.a:$(OBJS)
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$(AR) -csru $@ $(OBJS)
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sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
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$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
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multi:
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$(MAKE) clean
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$(MAKE)
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mv minimap2 mm2-fast
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$(MAKE) clean
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$(MAKE) lhash=1
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mv minimap2 mm2-fast-lhash
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$(MAKE) clean
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$(MAKE) no_opt=1
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mv minimap2 mm2-fast-no-opt
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# SSE-specific targets on x86/x86_64
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ifeq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2)
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ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
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endif
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ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_extd2_sse2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
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ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
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$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
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# NEON-specific targets on ARM
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ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
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ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
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ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
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$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
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# other non-file targets
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clean:
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rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
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depend:
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(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
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# DO NOT DELETE
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align.o: minimap.h mmpriv.h bseq.h ksw2.h kalloc.h
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bseq.o: bseq.h kvec.h kalloc.h kseq.h
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chain.o: minimap.h mmpriv.h bseq.h kalloc.h
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esterr.o: mmpriv.h minimap.h bseq.h
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example.o: minimap.h kseq.h
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format.o: kalloc.h mmpriv.h minimap.h bseq.h
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hit.o: mmpriv.h minimap.h bseq.h kalloc.h khash.h
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index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
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kalloc.o: kalloc.h
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ksw2_extd2_sse.o: ksw2.h kalloc.h
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ksw2_exts2_sse.o: ksw2.h kalloc.h
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ksw2_extz2_sse.o: ksw2.h kalloc.h
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ksw2_ll_sse.o: ksw2.h kalloc.h
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kthread.o: kthread.h
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main.o: bseq.h minimap.h mmpriv.h ketopt.h
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map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h khash.h
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map.o: ksort.h
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misc.o: mmpriv.h minimap.h bseq.h ksort.h
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options.o: mmpriv.h minimap.h bseq.h
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pe.o: mmpriv.h minimap.h bseq.h kvec.h kalloc.h ksort.h
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sdust.o: kalloc.h kdq.h kvec.h ketopt.h sdust.h
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sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h
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splitidx.o: mmpriv.h minimap.h bseq.h
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