alphabet.h
assert_helpers.h
binary_sa_search.h
bitpack.h
blockwise_sa.h
diff_sample.h
ebwt.h
ebwt_search_backtrack.h
endian_swap.h
formats.h
hit.h
multikey_qsort.h
pat.h
random_source.h
ref_read.h
sequence_io.h
timer.h
tokenize.h
word_io.h
zbox.h
ccnt_lut.cpp
ebwt_build.cpp
ebwt_search.cpp
hit.cpp
ref_read.cpp
maq_convert/const.h
maq_convert/maqmap.h
maq_convert/read_bfq.h
maq_convert/algo.hh
maq_convert/const.c
maq_convert/maqmap.c
maq_convert/bowtie_convert.cpp
scripts/build_test.sh
scripts/make_c_elegans.sh
scripts/make_c_familiaris.sh
scripts/make_d_melanogaster.sh
scripts/make_e_coli.sh
scripts/make_h_sapiens.sh
scripts/make_m_musculus.sh
scripts/make_p_troglodytes.sh
scripts/make_s_cerevisiae.sh
scripts/gen_lookup_tables.pl
scripts/random_bowtie_tests.pl
indexes/e_coli.1.ebwt
indexes/e_coli.2.ebwt
indexes/e_coli.README
indexes/e_coli.rev.1.ebwt
indexes/e_coli.rev.2.ebwt
genomes/NC_008253.fna
reads/e_coli_1000.fa
reads/e_coli_1000.fq
AUTHORS
COPYING
Makefile
NEWS
VERSION