Heng Li
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f0c94d80d1
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r379: fixed compiling error
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2013-04-19 12:04:00 -04:00 |
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Heng Li
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be11e27e12
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r378: bugfix - wrong CIGAR
This is actually caused by a bug in SSE2-SW, where the query begin may be
smaller than the true one if there is an exact tandem repeat.
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2013-04-19 12:00:37 -04:00 |
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Heng Li
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3d8a8c1e37
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r374: fix - clipping penalty not always working
This only happens to gaps where mem underestimates the bandwidth without
considering the clipping penalty.
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2013-04-10 01:09:37 -04:00 |
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Heng Li
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e6c262594f
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bwa-sw: ditch stdaln
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2013-03-05 10:12:38 -05:00 |
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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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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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b621d3ae38
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r301: left-align indels
Don't know why the change is working...
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2013-02-27 00:42:19 -05:00 |
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Heng Li
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ea8f4f4d34
|
clean bill from valgrind
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2013-02-20 20:26:57 -05:00 |
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Heng Li
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557daabf38
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bugfix: bug in the new ksw.c
On my test data, one alignment is different, caused by polyA
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2013-02-12 17:48:46 -05:00 |
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Heng Li
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28a7d501f2
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updated to the latest ksw; NOT TESTED YET!!!
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2013-02-12 16:35:05 -05:00 |
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Heng Li
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d8e4d57956
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Don't use narrow band.
I may retry this feature if the profilter indicates that this greatly helps.
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2013-02-07 21:22:54 -05:00 |
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Heng Li
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14e6a7bdb9
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fixed a silly bug in ksw_extend()
Query return value is assigned to the target variable and vice versa...
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2013-02-05 17:29:03 -05:00 |
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Heng Li
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1e16f3e701
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calling ksw_global(); ksw_extend() is buggy!
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2013-02-05 17:13:12 -05:00 |
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Heng Li
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86caae811e
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added comments
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2013-02-05 16:58:35 -05:00 |
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Heng Li
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1bc9712cd8
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explicitly use bit to keep bt matrix
This also simplifies backtracking.
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2013-02-05 16:28:15 -05:00 |
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Heng Li
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7e1466c885
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implemented NW backtrack
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2013-02-05 16:05:53 -05:00 |
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Heng Li
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d91e320972
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towards reimplementing banded NW alignment
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2013-02-05 12:06:56 -05:00 |
|
Heng Li
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788e9d1e3d
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fixed a couple of leaks; buggy atm
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2013-02-04 15:40:26 -05:00 |
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Heng Li
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ba18db1a9f
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sw extension works for the simplest case
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2013-02-04 12:37:38 -05:00 |
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Heng Li
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f83dea36d8
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no effective changes
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2013-02-03 18:16:43 -05:00 |
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Heng Li
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2093398231
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bugfix: the first line is wrong
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2013-02-03 17:47:57 -05:00 |
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Heng Li
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e8a1962efe
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code backup; it is wrong
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2013-02-03 17:25:40 -05:00 |
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Heng Li
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92b084e553
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reimplemented SW extension; not tested yet
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2013-02-02 16:38:21 -05:00 |
Heng Li
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182cb2e89c
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use standard SW when no SSE2
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2011-11-19 19:38:21 -05:00 |
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Heng Li
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c8c79ef024
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mate rescue seems working (not MT)
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2011-11-06 16:20:40 -05:00 |