-
b4c38bcc1c
append fasta/q comment
Heng Li
2013-02-23 16:57:34 -0500
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33236de32e
a bit more error message
Heng Li
2013-02-23 16:44:02 -0500
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ee4540c394
support read group in bwa-mem
Heng Li
2013-02-23 16:41:44 -0500
-
cfa7165036
cleanup index loading code
Heng Li
2013-02-23 16:10:48 -0500
-
67543f19a1
code refactoring
Heng Li
2013-02-23 15:55:55 -0500
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e613195e17
moved some common code to bwa.{c,h}
Heng Li
2013-02-23 15:30:46 -0500
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3c330d5049
for another round of code cleanup
Heng Li
2013-02-23 15:12:26 -0500
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d460f2ec9e
bugfix in multi-threaded bwa-mem
Heng Li
2013-02-23 14:48:54 -0500
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a19ab654df
no effective change
Heng Li
2013-02-23 14:21:19 -0500
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dd85c528d6
an alternative bwt_invPsi() implementation
Heng Li
2013-02-23 13:59:18 -0500
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904c3205c0
removed a few unused variables
Heng Li
2013-02-23 13:26:50 -0500
-
6230f86799
merged bwtmisc.c to bwtindex.c
Heng Li
2013-02-22 17:23:34 -0500
-
545fb87feb
removed another part related to color-space
Heng Li
2013-02-22 17:15:57 -0500
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f122fad562
minor code clean up
Heng Li
2013-02-22 17:09:40 -0500
-
17c123d65a
pring paired-end SAM
Heng Li
2013-02-22 16:38:48 -0500
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ba15b787cb
rework PE mapq; don't know if better
Heng Li
2013-02-22 14:47:57 -0500
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6c1a113753
mate-SW for all high-scoring hits
Heng Li
2013-02-22 13:26:23 -0500
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38fc5c8822
reduce mapQ when a read is moved
Heng Li
2013-02-22 12:54:42 -0500
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6a16edc15e
tuning PE mapQ
Heng Li
2013-02-22 12:47:26 -0500
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c0093264de
wrong logic: paired mapQ should <q_pe
Heng Li
2013-02-22 12:34:46 -0500
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c5ce72f593
scoring pairs by score, not by errors
Heng Li
2013-02-22 12:10:20 -0500
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ed08d08f36
fixed bugs caused by interger overflow
Heng Li
2013-02-22 11:17:31 -0500
-
dfc63acc11
bugfix: another ">" vs. "<" bug
Heng Li
2013-02-22 11:06:36 -0500
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d5820177c6
bugfix: wrong mate-sw qry coor for rev
Heng Li
2013-02-22 11:02:14 -0500
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81fe6f8e38
bugfix: a typo leading to wrong pairing
Heng Li
2013-02-22 10:57:07 -0500
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58e4cc207f
bugfix: 1) fill seedcov; 2) pairing not working
Heng Li
2013-02-21 21:26:01 -0500
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d4cf6d97a6
bugfix: memory leak
Heng Li
2013-02-21 15:04:31 -0500
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a578688fa8
generate multiple alignments from one chain
Heng Li
2013-02-21 14:58:51 -0500
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cfbc4c89e3
perform extension when there are, say, 20bp tandem
Heng Li
2013-02-21 14:34:10 -0500
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54da54ffd4
extend more seeds (and thus slower...)
Heng Li
2013-02-21 12:52:00 -0500
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f8829318cf
weakened the chain filter
Heng Li
2013-02-21 12:25:20 -0500
-
84a328764a
bugfix: mis-chaining caused by integer overflow
Heng Li
2013-02-21 11:42:30 -0500
-
a9cae8c9af
minor changes
Heng Li
2013-02-21 10:39:17 -0500
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41624fb347
bugfix: choosing the worse instead of the best
Heng Li
2013-02-20 20:43:22 -0500
-
ea8f4f4d34
clean bill from valgrind
Heng Li
2013-02-20 20:26:57 -0500
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5626fe29b7
Well, at least output sth
Heng Li
2013-02-20 19:11:44 -0500
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a7d574d125
backup comments
Heng Li
2013-02-20 01:11:38 -0500
-
688872fb1b
code backup
Heng Li
2013-02-19 00:50:39 -0500
-
66585b7982
code backup
Heng Li
2013-02-18 16:33:06 -0500
-
f0a6285aba
perform mate-SW for some suboptimal alignments
Heng Li
2013-02-16 11:52:04 -0500
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ea9fc7df48
keep the number of SW performed
Heng Li
2013-02-16 11:03:27 -0500
-
8ee464478a
matesw working; for testing only
Heng Li
2013-02-16 10:48:50 -0500
-
fe2236f6fe
code backup
Heng Li
2013-02-16 10:09:30 -0500
-
5f8c6efbc3
forbid x-bounary bns_get_seq(); code backup
Heng Li
2013-02-16 09:48:44 -0500
-
df1ff2b36e
better and proper way to infer orinentation
Heng Li
2013-02-14 12:59:32 -0500
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688b524cdf
code backup; tired..
Heng Li
2013-02-13 23:55:56 -0500
-
87d619a21f
minor code simplification
Heng Li
2013-02-13 23:16:16 -0500
-
557daabf38
bugfix: bug in the new ksw.c
Heng Li
2013-02-12 17:48:46 -0500
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28a7d501f2
updated to the latest ksw; NOT TESTED YET!!!
Heng Li
2013-02-12 16:35:05 -0500
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604e3d8da1
code backup; to upgrade ksw.{c,h}
Heng Li
2013-02-12 16:15:26 -0500
-
325ba8213b
move mark primary to worker1()
Heng Li
2013-02-12 15:54:55 -0500
-
cd0969332f
keep track of the "parent" of a secondary
Heng Li
2013-02-12 15:52:23 -0500
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22b79b3475
mark primary, instead of dropping secondary
Heng Li
2013-02-12 15:34:44 -0500
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2fc469d0c9
code backup
Heng Li
2013-02-12 12:09:36 -0500
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cfdc938fc3
to exclude "test64"
Heng Li
2013-02-12 10:39:16 -0500
-
95d18449b3
merge bseq.{h,c} to utils.{h,c}
Heng Li
2013-02-12 10:36:15 -0500
-
6ad5a3c086
removed color-space support
Heng Li
2013-02-12 10:21:17 -0500
-
e5ab59db53
Multiple changes:
Heng Li
2013-02-12 09:50:28 -0500
-
13288e2dcd
code backup
Heng Li
2013-02-12 09:22:47 -0500
-
dcb190069a
PE NOT working, yet
Heng Li
2013-02-11 16:10:14 -0500
-
99907c98fb
separated and improved SAM printing code
Heng Li
2013-02-11 15:29:03 -0500
-
b6006cbe9d
skip orientations that are much smaller than best
Heng Li
2013-02-11 13:44:39 -0500
-
4431e359e2
analyze isize distribution
Heng Li
2013-02-11 12:15:12 -0500
-
987d4b4205
fixed a stupid bug in fastq reading
Heng Li
2013-02-11 11:27:35 -0500
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59eaf650ac
code backup
Heng Li
2013-02-11 10:59:38 -0500
-
f4c0672800
move sort_and_dedup() to worker1()
Heng Li
2013-02-10 12:55:19 -0500
-
c310fb7424
a little refactoring for PE support
Heng Li
2013-02-10 12:24:33 -0500
-
cb55617f50
added a new line
Heng Li
2013-02-08 22:12:18 -0500
-
95a79afe71
command-line prompt
Heng Li
2013-02-08 22:11:44 -0500
-
829664d6b5
missing identical hits; improved sub_n
Heng Li
2013-02-08 17:55:35 -0500
-
b2c7148dc9
consider the number of suboptimal hits
Heng Li
2013-02-08 17:20:44 -0500
-
39607065e0
allow more seeds to be seen (thus slower..)
Heng Li
2013-02-08 16:56:28 -0500
-
2848d3045a
more accurate chain weight
Heng Li
2013-02-08 15:34:25 -0500
-
220fc39e9d
the previous change does not work... Fixed.
Heng Li
2013-02-08 14:51:24 -0500
-
fdb0a7405f
better dealing with microrepeat
Heng Li
2013-02-08 14:46:57 -0500
-
057b292dde
exclude identical hits
Heng Li
2013-02-08 14:18:39 -0500
-
1bf1a674a8
minor improvement to mapQ
Heng Li
2013-02-08 13:43:15 -0500
-
245505deed
minor improvement to mapQ approx.
Heng Li
2013-02-07 22:09:58 -0500
-
d8e4d57956
Don't use narrow band.
Heng Li
2013-02-07 21:22:54 -0500
-
d890c7997c
better treatment for micro-repeat
Heng Li
2013-02-07 21:20:36 -0500
-
45b0d3423a
bugfix: when no seed hits found
Heng Li
2013-02-07 20:07:31 -0500
-
cd6bd524d4
discard internal seeds shorter than half
Heng Li
2013-02-07 19:50:37 -0500
-
83a49f3210
compute mapQ; extend from the longest seed
Heng Li
2013-02-07 17:15:45 -0500
-
6ba11ab68c
no effective changes
Heng Li
2013-02-07 16:42:01 -0500
-
ff3fea115c
write soft clip; added debugging code
Heng Li
2013-02-07 16:27:11 -0500
-
27fdf6397d
single-end working! no mapQ, though
Heng Li
2013-02-07 15:52:36 -0500
-
49f2bcc015
CIGAR is wrong, but the rest is okay
Heng Li
2013-02-07 14:57:22 -0500
-
1fd51fc3f7
code backup
Heng Li
2013-02-07 14:36:18 -0500
-
bfeb37c4de
code backup
Heng Li
2013-02-07 13:29:01 -0500
-
5dc398cdef
start to write CLI
Heng Li
2013-02-07 13:13:43 -0500
-
a09db69037
In bwtsw, replace the batch seq-reader with bseq
Heng Li
2013-02-06 17:12:27 -0500
-
901d28d5f5
code backup
Heng Li
2013-02-06 15:03:09 -0500
-
5a0b32bfd2
updated to the latest kseq.h
Heng Li
2013-02-06 14:38:40 -0500
-
a9292d674d
a bit code cleanup
Heng Li
2013-02-06 13:59:32 -0500
-
e65b2096f7
removed useless members
Heng Li
2013-02-06 12:25:49 -0500
-
797a8c147e
sorting chains while filtering chains
Heng Li
2013-02-05 21:58:33 -0500
-
a61288c768
separate CIGAR generation
Heng Li
2013-02-05 21:49:19 -0500
-
14e6a7bdb9
fixed a silly bug in ksw_extend()
Heng Li
2013-02-05 17:29:03 -0500
-
1e16f3e701
calling ksw_global(); ksw_extend() is buggy!
Heng Li
2013-02-05 17:13:12 -0500
-
86caae811e
added comments
Heng Li
2013-02-05 16:58:35 -0500