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
34ed85d46a
optionally print the postions of long indels
2017-07-08 20:16:25 -04:00
2f11a63b22
script to collect alignment stats
2017-07-08 20:01:36 -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
d1f518e3ca
for clarity
2017-07-04 11:56:50 -04:00
6b584a1235
added README
2017-07-04 11:47:29 -04:00
8fff901e53
added test data
2017-07-04 10:56:48 -04:00
a65e557a7c
Merge branch 'dev'
2017-07-03 13:19:17 -04:00
e07daad7ad
r153: sam primary record not set sometimes
2017-07-03 13:18:57 -04:00
6ead8af104
Merge branch 'dev' into 'master'
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Fixed bugs when reporting secondary alignments
See merge request !1
2017-07-03 16:17:08 +00:00
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
696ebce66e
backup; still buggy
2017-07-03 00:52:00 -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
67cad9dff3
added limitations
2017-07-01 12:11:56 -04:00
a92bd75b7b
make the table fit 80 columns
2017-07-01 11:54:07 -04:00
02145b2166
explain option -d
2017-07-01 11:48:37 -04:00
3c45d84012
added license
2017-07-01 11:39:19 -04:00
b2ce3f9ed0
get rid of two more new lines
2017-07-01 11:37:58 -04:00
5ebe868db5
added two more new lines
2017-07-01 11:32:49 -04:00
cb6c277c62
removed unnecessary empty lines
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On linux, these empty lines count.
2017-07-01 11:31:32 -04:00
b883d132e2
no effective change
2017-07-01 11:26:23 -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
d4301736b8
more manpage
2017-07-01 00:23:46 -04:00
41efd03d7a
r129: fixed memory leak caused by qualities
2017-06-30 23:48:00 -04:00
10910b72d1
backup
2017-06-30 23:31:38 -04:00
d118cafd25
added man page
2017-06-30 23:30:17 -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
Heng Li