7babb54e4c
drop smem based mapping algorithm
...
While we can compute smems very efficiently, there is still a long way to get
the alignment. On simulated data, this smem-based algorithm is 4X faster than
bwasw and twice as fast as bowtie2, but the accuracy is far lower than bwasw
and even lower than bowtie2 in the high-mapQ range. I am kind of sure that if
we continue to increase the mapping accuracy, the speed will approach to bwasw,
if not slower.
Smem-based mapping algorithm is still interesting, but given that I am short of
time, I will not explore it further.
2011-10-27 10:56:09 -04:00
7467671c30
minor change
2011-10-25 21:39:38 -04:00
e890b8ac2e
preliminary code to generate fake sam
2011-10-25 19:45:55 -04:00
55059443bd
print msg to stderr; output more in fastmap
2011-10-25 15:06:13 -04:00
7664795ffb
fixed a minor issue about +/-1
2011-10-25 13:00:41 -04:00
7168f5c10a
updated revision number
2011-10-25 12:50:19 -04:00
4813257d4f
remove debugging code
2011-10-25 12:38:33 -04:00
f56edd07dd
forward-backward search seems working
2011-10-25 12:31:36 -04:00
aabb807734
concatenate for-rev sequences in the end
2011-10-25 11:22:08 -04:00
ca809a44d9
build .pac in memory; prepare for further changes
2011-10-25 10:27:13 -04:00
7626595e3a
backup the current debugging code; more changes
2011-10-25 10:03:57 -04:00
22c2252e15
added bidirectional bwt; seems buggy
2011-10-25 00:22:28 -04:00
7b4266a6e5
bugfix: integer overflow and strand error in sampe
2011-10-24 17:07:12 -04:00
b59fd2bf47
fixed an integer overflow
2011-10-24 14:39:57 -04:00
8f3c780552
fixed a potential int overflow
2011-10-24 14:22:39 -04:00
1f970b4557
updated revision number
2011-10-24 14:14:42 -04:00
eed46e802a
fixed a bug about reverse alignment
2011-10-24 14:09:05 -04:00
b204437c7e
fixed negative mapping quality; still byggy
2011-10-24 14:00:36 -04:00
8512b55ce3
bwasw works on a couple of sequences
2011-10-24 13:42:32 -04:00
4c43c5914d
this is better; but still buggy
2011-10-24 11:50:11 -04:00
29c3acfb31
not segfault immediately; but buggy
2011-10-24 09:36:52 -04:00
b3397a1f14
changes to bwa-sw for the 64-bit support; unfinish
2011-10-21 13:32:45 -04:00
26b77eabef
updated version number
2011-10-21 12:32:00 -04:00
1cb409aaf2
use forward-only pac to reduce memory
2011-10-21 12:03:14 -04:00
fe9da3c704
allow to pac forward strand only
2011-10-21 10:57:12 -04:00
66629512d9
more carefully computed the availableWords
2011-10-20 23:49:03 -04:00
ec307a10e6
PE seems working; more testing needed
2011-10-20 17:45:41 -04:00
098f44cd51
nothing
2011-10-20 16:26:14 -04:00
156852b1dd
no change
2011-10-20 16:15:16 -04:00
2d2db5d50f
aln seems working
2011-10-20 16:13:35 -04:00
46123639cf
removed reverse pac; bwa is not working right now
2011-10-20 12:09:35 -04:00
b96f180a15
move bwt_gen/* to the root directory
2011-10-20 11:56:24 -04:00
70da24e177
restructure bns_fasta2bntseq() for further changes
2011-10-20 11:53:44 -04:00
b7e8c4c5aa
fixed a bug in 2occ4()
2011-10-20 11:23:23 -04:00
d6155ecf90
fixed a couple of gcc warnings
2011-10-19 17:45:27 -04:00
c948c647a0
make changes to bwt.c
2011-10-19 17:42:42 -04:00
b6d807b0b7
minor changes in case something goes wrong
2011-10-19 13:50:50 -04:00
1f02acbe09
added a few assertions
2011-10-19 00:26:56 -04:00
573ad0c98f
merge bwt_gen.h to bwt_gen.c
2011-10-18 23:48:46 -04:00
95b1ab7e96
first attempt to make bwt_gen work for >4GB seq
2011-10-18 23:41:26 -04:00
3114edcb7c
further code clean up
2011-10-18 16:41:44 -04:00
d2f357af3a
a little bit code clean up
2011-10-18 16:39:18 -04:00
d70754e234
update revision number
2011-10-14 10:32:31 -04:00
80e02281d5
minor change
2011-10-14 10:31:48 -04:00
2255c4cd4b
fixed a long existing bug
...
This bug may cause segfault (though never to me) and lead to missing
suboptimal hits. But the top hits should not be affected.
2011-10-12 00:05:01 -04:00
beedc988f0
Merge pull request #5 from tobiasmarschall/master
...
xa2multi.pl: reverse sequence and phred if orientations differ between primary and secondary alignment
2011-09-07 05:55:39 -07:00
3536e2113c
Bugfix: reverse (complement) sequence and phred string if alternative alignment has different orientation than primary alignment
2011-09-07 14:31:28 +02:00
4f7734eb97
Merge pull request #2 from RoelKluin/master
...
Filter Casava 1.8 flagged sequences with bwa aln -Y
2011-07-10 12:27:55 -07:00
db59a605d1
Remove sequences marked to be filtered by Casava-1.8 with bwa aln -Y
...
In Casava 1.8 the fastq output changed. e.g.
@EAS139:136:FC706VJ:2:5:1000:12850 1:Y:18:ATCACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
BBBBCCCC?<A?BC?7@@???????DBBA@@@@A@@
The part after the space, treated as comment by bwa, contains the fields:
<read number>:<is filtered>:<control number>:<barcode sequence>
With `Y' Casava indicates that a sequence should be filtered. This patch
enables bwa, with an -Y flag, to filter these sequences.
Signed-off-by: Roel Kluin <roel.kluin@gmail.com>
2011-07-10 17:04:06 +02:00
8f115a8e00
Revert "In Casava 1.8 the fastq output changed, the name had a space which bwa"
...
This reverts commit 36cd4f9882
2011-07-10 16:40:42 +02:00
Heng Li
Tobias Marschall
Roel Kluin