Heng Li
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e0991d6a45
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r323: added Z-dropoff, a variant of blast's X-drop
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2013-03-05 00:34:33 -05:00 |
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Heng Li
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59bc9341f6
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code backup; more changes coming later
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2013-03-04 17:29:07 -05:00 |
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Heng Li
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35fb7f9fdf
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r315: move kopen.o out of libbwa.a
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2013-03-01 11:47:51 -05:00 |
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Heng Li
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3e4a178e08
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r314: cleanup bwamem API
Don't modify input sequences; more documentations
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2013-03-01 11:14:51 -05:00 |
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Heng Li
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6a4d8c79d8
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r309: bugfix - soft clipping missing in example.c
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2013-02-27 22:45:18 -05:00 |
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Heng Li
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df7c3f0000
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r308: added a new API to convert region to CIGAR
and an example program demonstrating how to do single-end alignment in <50
lines of C code.
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2013-02-27 22:28:29 -05:00 |
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Heng Li
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4bb0bdddca
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r306: introduce clipping penalty
More clipping leads to more severe reference bias. We should not clip the
alignment unless necessary.
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2013-02-27 21:13:39 -05:00 |
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Heng Li
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c6b226d719
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r292: fixed a very stupid bug on CLI
I was thinking 0x10 or 16, but wrote 0x16...
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2013-02-26 12:49:48 -05:00 |
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Heng Li
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20aa848b3c
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r279: for PE mapq, consider the number of pairs
If there are a lot of proper pairs, it is more likely that the best pair is
wrong.
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2013-02-25 13:00:35 -05:00 |
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Heng Li
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9957e04590
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r278: don't perform too many mate-sw
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2013-02-25 11:56:02 -05:00 |
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Heng Li
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5ead86acd3
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optionally mark split hit as secondary
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2013-02-25 11:18:35 -05:00 |
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Heng Li
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85775c3384
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output multiple hits
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2013-02-24 13:23:43 -05:00 |
|
Heng Li
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6bdccf2a8a
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added a bit documentation
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2013-02-24 13:09:29 -05:00 |
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Heng Li
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ee59a13109
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simplified bwamem.h
Hide mem_seed_t and mem_chain_t. Don't expose unnecessary routines.
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2013-02-24 12:17:29 -05:00 |
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Heng Li
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e613195e17
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moved some common code to bwa.{c,h}
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2013-02-23 15:30:46 -05:00 |
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Heng Li
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17c123d65a
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pring paired-end SAM
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2013-02-22 16:38:48 -05:00 |
|
Heng Li
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a578688fa8
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generate multiple alignments from one chain
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2013-02-21 14:58:51 -05:00 |
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Heng Li
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54da54ffd4
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extend more seeds (and thus slower...)
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2013-02-21 12:52:00 -05:00 |
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Heng Li
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5626fe29b7
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Well, at least output sth
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2013-02-20 19:11:44 -05:00 |
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Heng Li
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688872fb1b
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code backup
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2013-02-19 00:50:39 -05:00 |
|
Heng Li
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66585b7982
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code backup
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2013-02-18 16:33:06 -05:00 |
|
Heng Li
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df1ff2b36e
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better and proper way to infer orinentation
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2013-02-14 12:59:32 -05:00 |
|
Heng Li
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604e3d8da1
|
code backup; to upgrade ksw.{c,h}
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2013-02-12 16:15:26 -05:00 |
|
Heng Li
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cd0969332f
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keep track of the "parent" of a secondary
|
2013-02-12 15:52:23 -05:00 |
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Heng Li
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22b79b3475
|
mark primary, instead of dropping secondary
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2013-02-12 15:34:44 -05:00 |
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Heng Li
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95d18449b3
|
merge bseq.{h,c} to utils.{h,c}
I do not like many small files.
|
2013-02-12 10:36:15 -05:00 |
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Heng Li
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99907c98fb
|
separated and improved SAM printing code
This is for the PE mode. The routines may also be useful for bwa-sw, but
probably I won't change the old code.
|
2013-02-11 15:29:03 -05:00 |
|
Heng Li
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59eaf650ac
|
code backup
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2013-02-11 10:59:38 -05:00 |
|
Heng Li
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829664d6b5
|
missing identical hits; improved sub_n
|
2013-02-08 17:55:35 -05:00 |
|
Heng Li
|
b2c7148dc9
|
consider the number of suboptimal hits
|
2013-02-08 17:20:44 -05:00 |
|
Heng Li
|
39607065e0
|
allow more seeds to be seen (thus slower..)
|
2013-02-08 16:56:28 -05:00 |
|
Heng Li
|
fdb0a7405f
|
better dealing with microrepeat
|
2013-02-08 14:46:57 -05:00 |
|
Heng Li
|
1bf1a674a8
|
minor improvement to mapQ
|
2013-02-08 13:43:15 -05:00 |
|
Heng Li
|
bfeb37c4de
|
code backup
|
2013-02-07 13:29:01 -05:00 |
|
Heng Li
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5dc398cdef
|
start to write CLI
|
2013-02-07 13:13:43 -05:00 |
|
Heng Li
|
5a0b32bfd2
|
updated to the latest kseq.h
|
2013-02-06 14:38:40 -05:00 |
|
Heng Li
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a9292d674d
|
a bit code cleanup
|
2013-02-06 13:59:32 -05:00 |
|
Heng Li
|
e65b2096f7
|
removed useless members
|
2013-02-06 12:25:49 -05:00 |
|
Heng Li
|
a61288c768
|
separate CIGAR generation
|
2013-02-05 21:49:19 -05:00 |
|
Heng Li
|
d6a73c9171
|
chain filtering apparently working
|
2013-02-05 00:17:20 -05:00 |
|
Heng Li
|
9d0cdb2d3c
|
unfinished chain filter
|
2013-02-04 17:23:06 -05:00 |
|
Heng Li
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f27bd18f20
|
check if every seed is included; not used for now
|
2013-02-04 15:09:47 -05:00 |
|
Heng Li
|
5bfa45a69b
|
write the mem_aln_t struct
|
2013-02-04 15:02:56 -05:00 |
|
Heng Li
|
ba18db1a9f
|
sw extension works for the simplest case
|
2013-02-04 12:37:38 -05:00 |
|
Heng Li
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d25a87cc50
|
code backup
|
2013-02-02 15:14:24 -05:00 |
|
Heng Li
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00e5302219
|
routine to get subsequence from 2-bit pac
|
2013-02-01 16:39:50 -05:00 |
|
Heng Li
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f8f3b7577a
|
code cleanup; added a missing file
|
2013-02-01 14:38:44 -05:00 |
|
Heng Li
|
620ad6e5b9
|
reseed long SMEMs
|
2013-02-01 14:20:38 -05:00 |
|
Heng Li
|
8977737460
|
basic chaining working
Definitely suboptimal in a lot of corner cases...
|
2013-01-31 16:26:05 -05:00 |
|
Heng Li
|
6c19c9640c
|
code backup
|
2013-01-31 15:55:22 -05:00 |
|
Heng Li
|
91debf412b
|
move smem iterators to bwamem.{c,h}
|
2013-01-31 13:59:48 -05:00 |