Add native gzip/bzip2 support to Bowtie 1.01
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SeqAn-1.1
doc
genomes
indexes
reads
scripts
third_party
.gitignore
AUTHORS
LICENSE
MANUAL
MANUAL.markdown
Makefile
NEWS
README
TUTORIAL
VERSION
aligner.h
aligner_0mm.h
aligner_1mm.h
aligner_23mm.h
aligner_metrics.h
aligner_seed_mm.h
alphabet.cpp
alphabet.h
annot.cpp
annot.h
assert_helpers.h
auto_array.h
binary_sa_search.h
bitpack.h
bitset.h
blockwise_sa.h
bowtie
bowtie-align-l
bowtie-align-s
bowtie-build
bowtie-build-l
bowtie-build-s
bowtie-inspect
bowtie-inspect-l
bowtie-inspect-s
bowtie_build_main.cpp
bowtie_inspect.cpp
bowtie_main.cpp
btypes.h
ccnt_lut.cpp
chaincat.cpp
color.cpp
color.h
color_dec.cpp
color_dec.h
diff_sample.h
ebwt.cpp
ebwt.h
ebwt_build.cpp
ebwt_search.cpp
ebwt_search_backtrack.h
ebwt_search_util.cpp
ebwt_search_util.h
edit.cpp
edit.h
endian_swap.h
fast_mutex.h
filebuf.h
formats.h
hit.cpp
hit.h
hit_set.cpp
hit_set.h
log.cpp
log.h
mm.h
multikey_qsort.h
pat.cpp
pat.h
pool.h
processor_support.h
qual.cpp
qual.h
random_source.h
random_test.cpp
range.h
range_cache.h
range_chaser.h
range_source.h
ref_aligner.cpp
ref_aligner.h
ref_read.cpp
ref_read.h
reference.h
refmap.cpp
refmap.h
row_chaser.h
sam.cpp
sam.h
search_1mm_phase1.c
search_1mm_phase2.c
search_23mm_phase1.c
search_23mm_phase2.c
search_23mm_phase3.c
search_exact.c
search_globals.h
search_seeded_phase1.c
search_seeded_phase2.c
search_seeded_phase3.c
search_seeded_phase4.c
sequence_io.h
shmem.cpp
shmem.h
str_util.h
threading.h
timer.h
tinythread.cpp
tinythread.h
tokenize.h
word_io.h
zbox.h

README

Bowtie: http://bowtie-bio.sf.net

 - See AUTHORS for information about who wrote Bowtie and its various
   components.
 - See LICENSE for license information.
 - See MANUAL for detailed information on how to use Bowtie.
 - See NEWS for information about changes in this and previous versions
   of Bowtie.
 - See TUTORIAL for a quick example to get you started with Bowtie.