66585b7982
code backup
2013-02-18 16:33:06 -05:00
95d18449b3
merge bseq.{h,c} to utils.{h,c}
...
I do not like many small files.
2013-02-12 10:36:15 -05:00
987d4b4205
fixed a stupid bug in fastq reading
2013-02-11 11:27:35 -05:00
59eaf650ac
code backup
2013-02-11 10:59:38 -05:00
cb55617f50
added a new line
2013-02-08 22:12:18 -05:00
95a79afe71
command-line prompt
2013-02-08 22:11:44 -05:00
39607065e0
allow more seeds to be seen (thus slower..)
2013-02-08 16:56:28 -05:00
cd6bd524d4
discard internal seeds shorter than half
2013-02-07 19:50:37 -05:00
ff3fea115c
write soft clip; added debugging code
2013-02-07 16:27:11 -05:00
1fd51fc3f7
code backup
2013-02-07 14:36:18 -05:00
5dc398cdef
start to write CLI
2013-02-07 13:13:43 -05:00
5a0b32bfd2
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
a9292d674d
a bit code cleanup
2013-02-06 13:59:32 -05:00
a61288c768
separate CIGAR generation
2013-02-05 21:49:19 -05:00
1e16f3e701
calling ksw_global(); ksw_extend() is buggy!
2013-02-05 17:13:12 -05:00
d6a73c9171
chain filtering apparently working
2013-02-05 00:17:20 -05:00
9d0cdb2d3c
unfinished chain filter
2013-02-04 17:23:06 -05:00
788e9d1e3d
fixed a couple of leaks; buggy atm
2013-02-04 15:40:26 -05:00
ba18db1a9f
sw extension works for the simplest case
2013-02-04 12:37:38 -05:00
d25a87cc50
code backup
2013-02-02 15:14:24 -05:00
00e5302219
routine to get subsequence from 2-bit pac
2013-02-01 16:39:50 -05:00
f8f3b7577a
code cleanup; added a missing file
2013-02-01 14:38:44 -05:00
620ad6e5b9
reseed long SMEMs
2013-02-01 14:20:38 -05:00
8977737460
basic chaining working
...
Definitely suboptimal in a lot of corner cases...
2013-01-31 16:26:05 -05:00
91debf412b
move smem iterators to bwamem.{c,h}
2013-01-31 13:59:48 -05:00
5a4a0c4173
a bit refactoring for further changes
2013-01-31 12:34:05 -05:00
6641788d38
preparation for further changes
2013-01-31 11:42:31 -05:00
bf65b6463a
fastmap: optionally output the original query seq
2011-11-24 19:44:21 -05:00
150bfbdef4
fixed a deadlock; SMEM iterator
2011-11-24 19:15:14 -05:00
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
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
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
Heng Li
Heng Li