biology/bowtie/bowtie-1.3.1

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.
Name		Date	Size	#Lines	LOC
..		03-May-2022	-
.github/workflows/	H	14-Sep-2021	-	109	107
doc/	H	03-May-2022	-	4,180	3,895
genomes/	H	14-Sep-2021	-	70,558	70,557
indexes/	H	03-May-2022	-	5	4
reads/	H	14-Sep-2021	-	107,011	107,000
scripts/	H	03-May-2022	-	9,205	7,282
.gitignore	H A D	14-Sep-2021	286	18	17
.travis.yml	H A D	14-Sep-2021	1.4 KiB	42	41
AUTHORS	H A D	14-Sep-2021	670	19	14
LICENSE	H A D	14-Sep-2021	8.4 KiB	74	44
MANUAL	H A D	14-Sep-2021	60 KiB	1,506	1,136
MANUAL.markdown	H A D	14-Sep-2021	70.5 KiB	2,157	1,474
Makefile	H A D	03-May-2022	12.6 KiB	458	378
NEWS	H A D	14-Sep-2021	38.4 KiB	745	682
README	H A D	14-Sep-2021	374	10	8
TUTORIAL	H A D	14-Sep-2021	6.2 KiB	154	113
VERSION	H A D	14-Sep-2021	6	2	1
aligner.h	H A D	14-Sep-2021	63.6 KiB	2,054	1,611
aligner_0mm.h	H A D	14-Sep-2021	10.5 KiB	373	332
aligner_1mm.h	H A D	14-Sep-2021	15 KiB	489	436
aligner_23mm.h	H A D	14-Sep-2021	23.7 KiB	686	611
aligner_metrics.h	H A D	14-Sep-2021	11.2 KiB	376	278
aligner_seed_mm.h	H A D	14-Sep-2021	52 KiB	1,388	1,304
alphabet.cpp	H A D	14-Sep-2021	13 KiB	314	217
alphabet.h	H A D	14-Sep-2021	4.8 KiB	223	129
assert_helpers.h	H A D	14-Sep-2021	8.6 KiB	261	234
binary_sa_search.h	H A D	14-Sep-2021	2.8 KiB	81	54
bitpack.h	H A D	14-Sep-2021	785	35	23
bitset.h	H A D	14-Sep-2021	11.9 KiB	525	332
blockwise_sa.h	H A D	14-Sep-2021	34.5 KiB	1,135	853
bowtie	H A D	03-May-2022	2.6 KiB	85	63
bowtie-build	H A D	03-May-2022	2.7 KiB	99	74
bowtie-inspect	H A D	03-May-2022	2.5 KiB	70	54
bowtie_build_main.cpp	H A D	14-Sep-2021	1.4 KiB	59	38
bowtie_inspect.cpp	H A D	14-Sep-2021	15 KiB	534	458
bowtie_main.cpp	H A D	14-Sep-2021	1.4 KiB	59	38
bt2_locks.cpp	H A D	14-Sep-2021	958	41	32
bt2_locks.h	H A D	14-Sep-2021	1.6 KiB	75	61
btypes.h	H A D	14-Sep-2021	736	33	25
ccnt_lut.cpp	H A D	14-Sep-2021	13.3 KiB	303	299
chaincat.cpp	H A D	14-Sep-2021	638	38	26
cpu_numa_info.cpp	H A D	14-Sep-2021	288	10	7
cpu_numa_info.h	H A D	14-Sep-2021	109	7	4
diff_sample.h	H A D	14-Sep-2021	32.3 KiB	1,110	846
ds.h	H A D	14-Sep-2021	86.4 KiB	4,287	2,566
ebwt.cpp	H A D	14-Sep-2021	2.2 KiB	86	65
ebwt.h	H A D	14-Sep-2021	139.4 KiB	4,402	3,376
ebwt_build.cpp	H A D	14-Sep-2021	21.7 KiB	645	565
ebwt_search.cpp	H A D	14-Sep-2021	114.4 KiB	3,464	3,110
ebwt_search.h	H A D	14-Sep-2021	2 KiB	93	63
ebwt_search_backtrack.h	H A D	14-Sep-2021	99.7 KiB	3,144	2,262
ebwt_search_util.cpp	H A D	14-Sep-2021	1 KiB	43	34
ebwt_search_util.h	H A D	14-Sep-2021	11.9 KiB	374	283
edit.cpp	H A D	14-Sep-2021	236	17	7
edit.h	H A D	14-Sep-2021	1.8 KiB	91	47
endian_swap.h	H A D	14-Sep-2021	2.9 KiB	119	83
fast_mutex.h	H A D	14-Sep-2021	6.8 KiB	249	174
filebuf.h	H A D	14-Sep-2021	17.3 KiB	807	522
formats.h	H A D	14-Sep-2021	414	35	26
hit.cpp	H A D	14-Sep-2021	7.4 KiB	302	267
hit.h	H A D	14-Sep-2021	35.7 KiB	1,360	936
hit_set.cpp	H A D	14-Sep-2021	1.5 KiB	64	47
hit_set.h	H A D	14-Sep-2021	8.2 KiB	438	262
log.cpp	H A D	14-Sep-2021	54	8	2
log.h	H A D	14-Sep-2021	392	28	20
ls.cpp	H A D	14-Sep-2021	3.5 KiB	143	113
ls.h	H A D	14-Sep-2021	11.7 KiB	334	232
mem_ids.h	H A D	14-Sep-2021	1.2 KiB	36	9
mm.h	H A D	14-Sep-2021	453	17	5
multikey_qsort.h	H A D	14-Sep-2021	36.6 KiB	1,226	943
pat.cpp	H A D	14-Sep-2021	31.4 KiB	1,240	983
pat.h	H A D	14-Sep-2021	26.8 KiB	1,111	671
pool.h	H A D	14-Sep-2021	8.2 KiB	400	278
processor_support.h	H A D	14-Sep-2021	2.2 KiB	67	39
qual.cpp	H A D	14-Sep-2021	3.2 KiB	67	58
qual.h	H A D	14-Sep-2021	3.7 KiB	156	113
random_source.h	H A D	14-Sep-2021	5.1 KiB	253	166
random_test.cpp	H A D	14-Sep-2021	933	49	39
range.h	H A D	14-Sep-2021	1.1 KiB	55	38
range_cache.h	H A D	14-Sep-2021	15 KiB	544	373
range_chaser.h	H A D	14-Sep-2021	6.8 KiB	271	186
range_source.h	H A D	14-Sep-2021	65.9 KiB	2,466	1,742
read.h	H A D	14-Sep-2021	12.5 KiB	457	302
ref_aligner.cpp	H A D	14-Sep-2021	1.4 KiB	66	34
ref_aligner.h	H A D	14-Sep-2021	178.7 KiB	5,087	4,049
ref_read.cpp	H A D	14-Sep-2021	7.8 KiB	274	219
ref_read.h	H A D	14-Sep-2021	6.1 KiB	258	196
reference.h	H A D	14-Sep-2021	22.1 KiB	724	580
row_chaser.h	H A D	14-Sep-2021	4.5 KiB	185	120
sam.cpp	H A D	14-Sep-2021	7.4 KiB	313	260
sam.h	H A D	14-Sep-2021	2.2 KiB	123	81
search_1mm_phase1.c	H A D	14-Sep-2021	1.6 KiB	68	48
search_1mm_phase2.c	H A D	14-Sep-2021	878	32	20
search_23mm_phase1.c	H A D	14-Sep-2021	1.3 KiB	48	33
search_23mm_phase2.c	H A D	14-Sep-2021	1.1 KiB	44	29
search_23mm_phase3.c	H A D	14-Sep-2021	1.7 KiB	68	42
search_exact.c	H A D	14-Sep-2021	747	28	17
search_globals.h	H A D	14-Sep-2021	369	23	10
search_seeded_phase1.c	H A D	14-Sep-2021	2.3 KiB	90	65
search_seeded_phase2.c	H A D	14-Sep-2021	2.9 KiB	100	73
search_seeded_phase3.c	H A D	14-Sep-2021	4.3 KiB	145	103
search_seeded_phase4.c	H A D	14-Sep-2021	2.8 KiB	94	63
sequence_io.h	H A D	14-Sep-2021	5.9 KiB	204	153
shmem.cpp	H A D	14-Sep-2021	691	38	17
shmem.h	H A D	14-Sep-2021	4.2 KiB	151	122
sstring.h	H A D	14-Sep-2021	75.4 KiB	3,501	2,179
str_util.h	H A D	14-Sep-2021	414	29	22
threading.h	H A D	14-Sep-2021	5.5 KiB	225	168
timer.h	H A D	14-Sep-2021	3.9 KiB	150	110
tinythread.cpp	H A D	14-Sep-2021	8.3 KiB	308	192
tinythread.h	H A D	14-Sep-2021	20.7 KiB	715	376
tokenize.h	H A D	14-Sep-2021	1.1 KiB	54	36
util.h	H A D	14-Sep-2021	1.7 KiB	66	34
word_io.h	H A D	14-Sep-2021	2.5 KiB	128	97
zbox.h	H A D	14-Sep-2021	2 KiB	80	64