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Merge branch 'chain-tune' into merge2

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Heng Li
2020-04-05 12:07:13 -04:00
parent ac3fcc339a f0c53e9948
commit 5917aa2f36
28 changed files with 2068 additions and 4528 deletions
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Makefile
+5 -29
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@@ -1,11 +1,12 @@
CXX= g++
CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall #-fsanitize=address -fno-omit-frame-pointer#-Winline
CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall
CPPFLAGS=
INCLUDES=
OBJS= Output.o CommandLines.o Process_Read.o Assembly.o kmer.o Hash_Table.o \
POA.o Correct.o Levenshtein_distance.o Overlaps.o Trio.o kthread.o Purge_Dups.o #ksw2_extz2_sse.o
OBJS= Output.o CommandLines.o Process_Read.o Assembly.o Hash_Table.o \
POA.o Correct.o Levenshtein_distance.o Overlaps.o Trio.o kthread.o Purge_Dups.o \
htab.o hist.o sketch.o anchor.o sys.o
EXE= hifiasm
LIBS= -lz -lpthread -lm #-fsanitize=address -fno-omit-frame-pointer
LIBS= -lz -lpthread -lm
ifneq ($(asan),)
CXXFLAGS+=-fsanitize=address
@@ -30,28 +31,3 @@ depend:
(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CPPFLAGS) $(DFLAGS) -- *.cpp)
# DO NOT DELETE
Assembly.o: Assembly.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
Assembly.o: CommandLines.h kmer.h Hash_Table.h khash.h POA.h Correct.h
Assembly.o: Levenshtein_distance.h Output.h Trio.h
CommandLines.o: CommandLines.h ketopt.h
Correct.o: Correct.h Hash_Table.h khash.h kmer.h Process_Read.h kseq.h
Correct.o: Overlaps.h kvec.h kdq.h CommandLines.h Levenshtein_distance.h
Correct.o: POA.h Assembly.h #ksw2.h
Hash_Table.o: Hash_Table.h khash.h kmer.h Process_Read.h kseq.h Overlaps.h
Hash_Table.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h
Hash_Table.o: POA.h ksort.h
Levenshtein_distance.o: Levenshtein_distance.h
Output.o: Output.h CommandLines.h
Overlaps.o: Overlaps.h kvec.h kdq.h ksort.h Process_Read.h kseq.h
Overlaps.o: CommandLines.h Purge_Dups.h
POA.o: POA.h Hash_Table.h khash.h kmer.h Process_Read.h kseq.h Overlaps.h
POA.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h
Process_Read.o: Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
kmer.o: kmer.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
main.o: CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
main.o: Assembly.h Levenshtein_distance.h
Trio.o: Trio.h khashl.h kthread.h Process_Read.h CommandLines.h
kthread.o: kthread.h
Purge_Dups.o: Purge_Dups.h Overlaps.h Hash_Table.h Correct.h ksort.h
#ksw2_extz2_sse.o: ksw2.h