Commit 624ab077 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.2.6

parent 133694bd

.gitignore

0 → 100644
+6 −0
Original line number Diff line number Diff line 
kma

kma_index

kma_shm

kma_update

*.o

*.a

KMA.c

deleted100644 → 0
+0 −18474

File deleted.

Preview size limit exceeded, changes collapsed.

KMA_index.c

deleted100644 → 0
+0 −4061

File deleted.

Preview size limit exceeded, changes collapsed.

KMAspecification.pdf

0 → 100644
+346 KiB

File added.

No diff preview for this file type.

View file

Makefile

+66 −12
Original line number Diff line number Diff line 
CFLAGS = -w -O3

BINS = kma kma_index kma_shm kma_update

CFLAGS = -Wall -O3 -std=c99

LIBS = align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o decon.o ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmers.o kmmap.o loadupdate.o makeindex.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o update.o updateindex.o updatescores.o valueshash.o vcf.o

PROGS = kma kma_index kma_shm kma_update



all: $(BINS)

.c .o:

	$(CC) $(CFLAGS) -c -o $@ $<



kma: KMA.c

	$(CC) $(CFLAGS) -o $@ $< -lm -lpthread -lz

all: $(PROGS)



kma_index: KMA_index.c

	$(CC) $(CFLAGS) -o $@ $< -lm -lz

kma: main.c libkma.a

	$(CC) $(CFLAGS) -o $@ main.c libkma.a -lm -lpthread -lz



kma_shm: KMA_SHM.c

	$(CC) $(CFLAGS) -o $@ $<

kma_index: kma_index.c libkma.a

	$(CC) $(CFLAGS) -o $@ kma_index.c libkma.a -lm -lz



kma_update: KMA_update.c

	$(CC) $(CFLAGS) -o $@ $<

kma_shm: kma_shm.c libkma.a

	$(CC) $(CFLAGS) -o $@ kma_shm.c libkma.a



kma_update: kma_update.c libkma.a

	$(CC) $(CFLAGS) -o $@ kma_update.c libkma.a



libkma.a: $(LIBS)

	$(AR) -csru $@ $(LIBS)



clean:

	$(RM) $(BINS)
 
	$(RM) $(LIBS) $(PROGS) libkma.a



align.o: align.h chain.h compdna.h hashmapindex.h nw.h stdnuc.h stdstat.h

alnfrags.o: alnfrags.h align.h ankers.h compdna.h hashmapindex.h qseqs.h threader.h updatescores.h

ankers.o: ankers.h compdna.h pherror.h qseqs.h

assembly.o: assembly.h align.h filebuff.h kmapipe.h pherror.h stdnuc.h stdstat.h threader.h

chain.o: chain.h penalties.h pherror.h stdstat.h

compdna.o: compdna.h pherror.h stdnuc.h

compkmers.o: compkmers.h pherror.h

compress.o: compress.h hashmap.h hashmapkma.h pherror.h valueshash.h

decon.o: decon.h compdna.h filebuff.h hashmapkma.h seqparse.h stdnuc.h qseqs.h updateindex.h

ef.o: ef.h assembly.h stdnuc.h vcf.h version.h

filebuff.o: filebuff.h pherror.h qseqs.h

frags.o: frags.h filebuff.h pherror.h qseqs.h

hashmap.o: hashmap.h hashtable.h pherror.h

hashmapindex.o: hashmapindex.h pherror.h stdnuc.h

hashmapkma.o: hashmapkma.h pherror.h

hashmapkmers.o: hashmapkmers.h pherror.h

hashtable.o: hashtable.h hashmapkma.h hashmapkmers.h pherror.h

index.o: index.h compress.h decon.h hashmap.h hashmapkma.h loadupdate.h makeindex.h pherror.h stdstat.h version.h

kma.o: kma.h ankers.h assembly.h chain.h hashmapkma.h kmers.h mt1.h penalties.h pherror.h qseqs.h runinput.h runkma.h savekmers.h sparse.h spltdb.h version.h

kmapipe.o: kmapipe.h pherror.h

kmers.o: kmers.h ankers.h compdna.h hashmapkma.h kmapipe.h pherror.h qseqs.h savekmers.h spltdb.h

kmmap.o: kmmap.h hashmapkma.h

loadupdate.o: loadupdate.h pherror.h hashmap.h hashmapkma.h updateindex.h

makeindex.o: makeindex.h compdna.h filebuff.h hashmap.h pherror.h qseqs.h seqparse.h updateindex.h

mt1.o: mt1.h assembly.h chain.h filebuff.h hashmapindex.h kmapipe.h nw.h penalties.h pherror.h printconsensus.h qseqs.h runkma.h stdstat.h vcf.h

nw.o: nw.h pherror.h stdnuc.h penalties.h

pherror.o: pherror.h

printconsensus.o: printconsensus.h assembly.h

qseqs.o: qseqs.h pherror.h

qualcheck.o: qualcheck.h compdna.h hashmap.h pherror.h stdnuc.h stdstat.h

runinput.o: runinput.h compdna.h filebuff.h pherror.h qseqs.h seqparse.h

runkma.o: runkma.h align.h alnfrags.h assembly.h chain.h compdna.h ef.h filebuff.h frags.h hashmapindex.h kmapipe.h nw.h pherror.h printconsensus.h qseqs.h stdnuc.h stdstat.h vcf.h

sam.o: sam.h nw.h pherror.h qseqs.h runkma.h

savekmers.o: savekmers.h ankers.h compdna.h hashmapkma.h penalties.h pherror.h qseqs.h stdnuc.h stdstat.h threader.h

seq2fasta.o: seq2fasta.h pherror.h qseqs.h runkma.h stdnuc.h

seqparse.o: seqparse.h filebuff.h qseqs.h

shm.o: shm.h pherror.h hashmapkma.h version.h

sparse.o: sparse.h compkmers.h hashtable.h kmapipe.h pherror.h runinput.h savekmers.h stdnuc.h stdstat.h

spltdb.o: spltdb.h align.h alnfrags.h assembly.h chain.h compdna.h ef.h filebuff.h frags.h hashmapindex.h kmapipe.h nw.h pherror.h printconsensus.h qseqs.h runkma.h stdnuc.h stdstat.h vcf.h

stdnuc.o: stdnuc.h

stdstat.o: stdstat.h

update.o: update.h hashmapkma.h pherror.h stdnuc.h

updateindex.o: updateindex.h compdna.h hashmap.h hashmapindex.h pherror.h qualcheck.h stdnuc.h pherror.h

updatescores.o: updatescores.h qseqs.h

valueshash.o: valueshash.h pherror.h

vcf.o: vcf.h assembly.h filebuff.h stdnuc.h stdstat.h version.h