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clean code

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This commit is contained in:
Haoyu Cheng
2019-12-26 02:26:24 -05:00
parent 7f9c73507d
commit 4ac9907e49
26 changed files with 1585 additions and 19325 deletions
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Makefile
+6 -7
View File
@@ -1,10 +1,10 @@
CXX= g++
CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Winline -Wall
CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall #-Winline
CPPFLAGS=
INCLUDES=
OBJS= Output.o CommandLines.o Process_Read.o Assembly.o kmer.o Hash_Table.o \
POA.o Correct.o Levenshtein_distance.o edlib.o Overlaps.o ksw2_extz2_sse.o
EXE= ccs_assembly
POA.o Correct.o Levenshtein_distance.o Overlaps.o #ksw2_extz2_sse.o
EXE= hifiasm
LIBS= -lz -lpthread -lm
ifneq ($(asan),)
@@ -37,7 +37,7 @@ Assembly.o: Levenshtein_distance.h Output.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 edlib.h Assembly.h ksw2.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
@@ -48,8 +48,7 @@ Overlaps.o: CommandLines.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
edlib.o: edlib.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 edlib.h
ksw2_extz2_sse.o: ksw2.h
main.o: Assembly.h Levenshtein_distance.h
#ksw2_extz2_sse.o: ksw2.h