Heng Li
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a01d758af6
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r206: mapq penalize short chains further
The old code penalized at the log() scale. Now added a linear-scaled factor. If
the chain consists of few minimizers, its quality is really not good.
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2017-07-26 11:50:04 -04:00 |
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Heng Li
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e9dc1ce2b6
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r205: when computing mapq, consider min_chain_sc
Not doing this was a mistake.
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2017-07-26 11:34:14 -04:00 |
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Heng Li
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00c6db5073
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r203: check more subopt aln if score small
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2017-07-25 20:02:44 -04:00 |
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Heng Li
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38aa66fa30
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r178: fixed integer overflow in mapq calculation
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2017-07-16 21:45:39 -04:00 |
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Heng Li
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b4280d186f
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r176: removed seedcov_ratio; changed default opt
min_seedcov_ratio is not used
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2017-07-12 12:47:46 -04:00 |
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Heng Li
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801bc84b01
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r169: output more accurate col. 10&11 to PAF
In r168, col.10 is smaller than what it should be. This confuses miniasm.
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2017-07-11 14:09:51 -04:00 |
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Heng Li
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782449975d
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r168: fixed a bug in long join: a[] not sorted
Also added length requirement for long join and changed -g in the ava mode
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2017-07-09 12:14:20 -04:00 |
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Heng Li
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1ac48556ae
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r167: long join threshold depends on gap
also caught a bug for reverse strand join
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2017-07-09 10:38:51 -04:00 |
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Heng Li
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38b2830e18
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r161: filter bad seeds; changed default -g/-r
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2017-07-08 13:31:27 -04:00 |
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Heng Li
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e07daad7ad
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r153: sam primary record not set sometimes
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2017-07-03 13:18:57 -04:00 |
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Heng Li
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b625247300
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r150: mm_sync_regs() doesn't work with negative id
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2017-07-03 11:36:34 -04:00 |
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Heng Li
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2e4fd9f1d0
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r148: revamped regs handling after cigar
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2017-07-03 10:44:26 -04:00 |
|
Heng Li
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696ebce66e
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backup; still buggy
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2017-07-03 00:52:00 -04:00 |
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Heng Li
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e06c342659
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r146: in filtering, drop children if parent out
This has been causing several segfaults.
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2017-07-03 00:28:12 -04:00 |
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Heng Li
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632b8638d2
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r144: adjust primary aln after cigar
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2017-07-02 22:43:02 -04:00 |
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Heng Li
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2b45ba7a0b
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r143: fixed a segfault and incorrect .parent
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2017-07-02 19:56:21 -04:00 |
|
Heng Li
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74d306a596
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fixed bug when retaining 2ndary aln; still buggy
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2017-07-02 19:08:30 -04:00 |
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Heng Li
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426c2975f6
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r126: filter by fraction of seed coverage
otherwise we may get too many poor overlap mappings.
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2017-06-30 22:15:45 -04:00 |
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Heng Li
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3a5486325a
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r123: fixed a mem leak; more presets
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2017-06-30 15:39:05 -04:00 |
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Heng Li
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646a746cdc
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r122: filter contained aln after DP extension
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2017-06-30 15:23:30 -04:00 |
|
Heng Li
|
08a61c3cfc
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r119: fixed a bug hidden by a previous bug
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2017-06-30 13:27:47 -04:00 |
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Heng Li
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1a903486b9
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r118: bugfix - regs unsorted before filtering
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2017-06-30 12:52:28 -04:00 |
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Heng Li
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52b4d8e2c9
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r115: set primary tag; still buggy
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2017-06-29 23:48:35 -04:00 |
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Heng Li
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11167f511b
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r112: output z-drop
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2017-06-29 22:08:46 -04:00 |
|
Heng Li
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4cd456b9ba
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r108: refactoring, move reg1 routines to hit.c
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2017-06-29 19:44:11 -04:00 |
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Heng Li
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ecedfe5788
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code refactoring for mm_reg1_t
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2017-06-29 19:35:38 -04:00 |