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prepare for further changes

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Heng Li
2020-06-06 21:55:41 -04:00
parent 97f6efc4da
commit afa93e4bbb
14 changed files with 459 additions and 465 deletions
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Makefile
+11 -10
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@@ -4,7 +4,7 @@ CPPFLAGS=
INCLUDES=
OBJS= 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 extract.o sys.o
htab.o hist.o sketch.o anchor.o extract.o overlap2.o sys.o
EXE= hifiasm
LIBS= -lz -lpthread -lm
@@ -34,17 +34,17 @@ depend:
Assembly.o: Assembly.h CommandLines.h Process_Read.h Overlaps.h kvec.h kdq.h
Assembly.o: Hash_Table.h htab.h POA.h Correct.h Levenshtein_distance.h
Assembly.o: kthread.h
Assembly.o: kthread.h utils.h
CommandLines.o: CommandLines.h ketopt.h
Correct.o: Correct.h Hash_Table.h htab.h Process_Read.h Overlaps.h kvec.h
Correct.o: kdq.h CommandLines.h Levenshtein_distance.h POA.h Assembly.h
Hash_Table.o: Hash_Table.h htab.h Process_Read.h Overlaps.h kvec.h kdq.h
Hash_Table.o: CommandLines.h ksort.h
Hash_Table.o: CommandLines.h ksort.h utils.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 CommandLines.h
Overlaps.o: Hash_Table.h htab.h Correct.h Levenshtein_distance.h POA.h
Overlaps.o: Purge_Dups.h
Overlaps.o: Purge_Dups.h utils.h
POA.o: POA.h Hash_Table.h htab.h Process_Read.h Overlaps.h kvec.h kdq.h
POA.o: CommandLines.h Correct.h Levenshtein_distance.h
Process_Read.o: Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
@@ -52,16 +52,17 @@ Purge_Dups.o: ksort.h Purge_Dups.h kvec.h kdq.h Overlaps.h Hash_Table.h
Purge_Dups.o: htab.h Process_Read.h CommandLines.h Correct.h
Purge_Dups.o: Levenshtein_distance.h POA.h kthread.h
Trio.o: khashl.h kthread.h kseq.h Process_Read.h Overlaps.h kvec.h kdq.h
Trio.o: CommandLines.h htab.h
Trio.o: CommandLines.h htab.h utils.h
anchor.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
anchor.o: ksort.h Hash_Table.h
anchor.o: ksort.h utils.h Hash_Table.h
extract.o: Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h khashl.h
extract.o: kseq.h
extract.o: kseq.h utils.h
hist.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
htab.o: kthread.h khashl.h kseq.h ksort.h htab.h Process_Read.h Overlaps.h
htab.o: kvec.h kdq.h CommandLines.h
htab.o: kvec.h kdq.h CommandLines.h utils.h
kthread.o: kthread.h
main.o: CommandLines.h Process_Read.h Overlaps.h kvec.h kdq.h Assembly.h
main.o: Levenshtein_distance.h htab.h
main.o: Levenshtein_distance.h utils.h
overlap2.o: utils.h CommandLines.h Overlaps.h kvec.h kdq.h
sketch.o: kvec.h htab.h Process_Read.h Overlaps.h kdq.h CommandLines.h
sys.o: htab.h Process_Read.h Overlaps.h kvec.h kdq.h CommandLines.h
sys.o: utils.h