b9b0b6f49c
r187: fixed non-terminated sam output ( #3 )
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Only happen to unmapped read, with quality, and in the SAM output
2017-07-18 15:20:29 -04:00
495a78e40a
Get documentation ready for release
2017-07-18 11:04:09 -04:00
71e2a97a4c
r180: changed -x asm5 settings
2017-07-18 00:00:36 -04:00
941059292e
r179: changed the preset for assembly alignment
2017-07-17 22:41:46 -04:00
38aa66fa30
r178: fixed integer overflow in mapq calculation
2017-07-16 21:45:39 -04:00
b4280d186f
r176: removed seedcov_ratio; changed default opt
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min_seedcov_ratio is not used
2017-07-12 12:47:46 -04:00
52caf79395
r175: halved max-chain-skip in the ava mode
2017-07-12 10:42:19 -04:00
eeeb2ffb68
r174: make max-chain-skip work
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The max-chain-skip heuristics did not work due to a bug. Without this
heuristics, chaining is too slow for long-read overlap.
2017-07-12 10:08:06 -04:00
33451aba45
r173: changed the debugging output format
2017-07-11 15:23:28 -04:00
cfa083a98b
r172: separated PacBio and ONT read overlapping
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HPC k-mer works better for PacBio, but worse for ONT. Interesting...
2017-07-11 15:12:35 -04:00
7598809577
r171: reduced log gap cost at chaining
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The cost is so large that it discards too many valid seeds without HPC k-mers.
This change may introduce false long gaps to reference mapping. We have another
mechanism mm_filter_bad_seeds() to protect against this. In addition, minimap2
is not that bad to have long gaps. Some other aligners are worse.
Still need tuning in future.
2017-07-11 14:57:49 -04:00
826c8ba892
r170: added a debugging flag
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something wrong with chaining
2017-07-11 14:47:35 -04:00
801bc84b01
r169: output more accurate col. 10&11 to PAF
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In r168, col.10 is smaller than what it should be. This confuses miniasm.
2017-07-11 14:09:51 -04:00
782449975d
r168: fixed a bug in long join: a[] not sorted
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Also added length requirement for long join and changed -g in the ava mode
2017-07-09 12:14:20 -04:00
1ac48556ae
r167: long join threshold depends on gap
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also caught a bug for reverse strand join
2017-07-09 10:38:51 -04:00
4ee3202539
r164: unmapped read not properly flagged
2017-07-08 18:16:18 -04:00
42846ce65d
r163: reduced long join score requirement
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because the chaining score is generally smaller with the last few commits.
2017-07-08 15:51:52 -04:00
3f6a0b0b5c
r162: improved chaining accuracy
2017-07-08 14:29:36 -04:00
38b2830e18
r161: filter bad seeds; changed default -g/-r
2017-07-08 13:31:27 -04:00
1fee5f8edc
r160: -O and -E accept two numbers
2017-07-08 11:34:52 -04:00
cc554aee43
r159: use two-piece gap penalty
2017-07-08 10:26:00 -04:00
9823317e8f
r158: optionally ignore base quality
2017-07-05 18:23:50 -04:00
e07daad7ad
r153: sam primary record not set sometimes
2017-07-03 13:18:57 -04:00
a94bc31311
r151: documentations
2017-07-03 12:11:07 -04:00
b625247300
r150: mm_sync_regs() doesn't work with negative id
2017-07-03 11:36:34 -04:00
53c4bf5e4f
r149: introduced debugging flags on CLI
2017-07-03 11:02:32 -04:00
2e4fd9f1d0
r148: revamped regs handling after cigar
2017-07-03 10:44:26 -04:00
e06c342659
r146: in filtering, drop children if parent out
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This has been causing several segfaults.
2017-07-03 00:28:12 -04:00
51cfb60520
r145: changed default -p from 2 to 0.8
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For long reads, secondary alignments can be very information.
2017-07-02 22:51:45 -04:00
632b8638d2
r144: adjust primary aln after cigar
2017-07-02 22:43:02 -04:00
2b45ba7a0b
r143: fixed a segfault and incorrect .parent
2017-07-02 19:56:21 -04:00
74d306a596
fixed bug when retaining 2ndary aln; still buggy
2017-07-02 19:08:30 -04:00
da90b614db
r141: replaced -b with -a (for SAM output)
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-b sounds like BAM. I like -a better.
2017-07-01 16:54:59 -04:00
2338e887d9
finished the first draft of manpage
2017-07-01 11:25:54 -04:00
a9f089f0aa
r131: wrong EOF test; make mb_size <= batch_size
2017-07-01 09:26:09 -04:00
41efd03d7a
r129: fixed memory leak caused by qualities
2017-06-30 23:48:00 -04:00
426c2975f6
r126: filter by fraction of seed coverage
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otherwise we may get too many poor overlap mappings.
2017-06-30 22:15:45 -04:00
d73bb28097
r125: changed CLI options
2017-06-30 19:08:47 -04:00
b08591c7a0
r124: a bit better CLI prompt
2017-06-30 15:46:52 -04:00
3a5486325a
r123: fixed a mem leak; more presets
2017-06-30 15:39:05 -04:00
646a746cdc
r122: filter contained aln after DP extension
2017-06-30 15:23:30 -04:00
fce87ce7bd
r121: output QUAL and unmapped to SAM
2017-06-30 14:40:54 -04:00
d11049eb32
r120: use max-scoring seg to control output
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much better now
2017-06-30 14:21:44 -04:00
08a61c3cfc
r119: fixed a bug hidden by a previous bug
2017-06-30 13:27:47 -04:00
1a903486b9
r118: bugfix - regs unsorted before filtering
2017-06-30 12:52:28 -04:00
5dcd8f8965
r117: fixed a bug in logic
2017-06-30 11:52:42 -04:00
91e1c4d6db
r116: fixed another bug caused by refactoring
2017-06-30 00:03:45 -04:00
52b4d8e2c9
r115: set primary tag; still buggy
2017-06-29 23:48:35 -04:00
c4871f380c
r114: make SAM output better
2017-06-29 23:08:41 -04:00
03267e8fa7
r113: fixed a sam header bug
2017-06-29 22:43:06 -04:00
Heng Li