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Makefile added makedepend Jul 1, 2014
README.md
bubble.c r162: cleanup graph simplification Sep 5, 2014
correct.c r158: reverted to r156 Sep 2, 2014
dfs.c r156: removed fastsim Aug 27, 2014
diff.c r81: use kthread to replace pthread Dec 9, 2013
fermi2.h r178: added trim depth; better in practice Jan 18, 2015
fermi2.js
fermi2.pl
khash.h
kseq.h
ksort.h
kstring.h separate unpack and sub Oct 16, 2013
ksw.c k76: ported "unitig" and "clean" from fermi1 Dec 6, 2013
ksw.h
kthread.c
kvec.h
mag.c
mag.h
main.c
match.c
priv.h
rld0.c
rld0.h
sa.c
seq.c
sgdp.md
sub.c r81: use kthread to replace pthread Dec 9, 2013
sys.c
unitig.c r170: the pre-rev not working in all cases Oct 30, 2014
unpack.c

README.md

Note: fermi2 is in fact not the successor of fermi. It drops the assembly component in fermi and focuses on the exploration of FMD-index as a graph. It relies on fermi or ropebwt2 for index construction.

Fermi2 is fairly incomplete, but some components are usable and to some extend better than fermi equivalent.

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