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NOT WORKING!!! added all k-mer counter

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Heng Li
2020-03-24 12:29:46 -04:00
parent 398e73022b
commit 64edb06e08
15 changed files with 628 additions and 237 deletions
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Makefile
+14 -10
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@@ -3,7 +3,8 @@ CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall
CPPFLAGS=
INCLUDES=
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
POA.o Correct.o Levenshtein_distance.o Overlaps.o Trio.o kthread.o \
yak-bbf.o yak-count.o yak-sys.o
EXE= hifiasm
LIBS= -lz -lpthread -lm
@@ -32,25 +33,28 @@ depend:
# DO NOT DELETE
Assembly.o: Assembly.h CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h
Assembly.o: kdq.h kmer.h Hash_Table.h khashl.h POA.h Correct.h
Assembly.o: Levenshtein_distance.h Output.h Trio.h
Assembly.o: kdq.h kmer.h Hash_Table.h khashl.h yak.h POA.h Correct.h
Assembly.o: Levenshtein_distance.h Output.h
CommandLines.o: CommandLines.h ketopt.h
Correct.o: Correct.h Hash_Table.h khashl.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
Correct.o: Overlaps.h kvec.h kdq.h CommandLines.h yak.h
Correct.o: Levenshtein_distance.h POA.h Assembly.h
Hash_Table.o: Hash_Table.h khashl.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
Hash_Table.o: kvec.h kdq.h CommandLines.h yak.h Correct.h
Hash_Table.o: Levenshtein_distance.h 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 Hash_Table.h khashl.h kmer.h Correct.h
Overlaps.o: CommandLines.h Hash_Table.h khashl.h kmer.h yak.h Correct.h
Overlaps.o: Levenshtein_distance.h POA.h
POA.o: POA.h Hash_Table.h khashl.h kmer.h Process_Read.h kseq.h Overlaps.h
POA.o: kvec.h kdq.h CommandLines.h Correct.h Levenshtein_distance.h
POA.o: kvec.h kdq.h CommandLines.h yak.h Correct.h Levenshtein_distance.h
Process_Read.o: Process_Read.h kseq.h Overlaps.h kvec.h kdq.h CommandLines.h
Trio.o: khashl.h kthread.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
Trio.o: CommandLines.h Trio.h kmer.h
Trio.o: CommandLines.h yak.h
kthread.o: kthread.h
main.o: CommandLines.h Process_Read.h kseq.h Overlaps.h kvec.h kdq.h
main.o: Assembly.h Levenshtein_distance.h
yak-bbf.o: yak.h
yak-count.o: CommandLines.h yak.h khashl.h kthread.h kseq.h
yak-sys.o: yak.h