b530ade333
r199: changed to linear gap cost for chaining
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The old cost doesn't penalize long gaps enough. Will also drop seeds close to
the edge in the next commit.
2017-07-25 15:35:10 -04:00
4bd7ebc39c
convert pbsim .maf to fasta
2017-07-25 13:54:58 -04:00
f81f37fef1
r197: allocate index seq names from kalloc
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to reduce malloc() overhead.
2017-07-24 19:36:05 -04:00
5c4d040b13
r191: warning if CLI index opt diff from prebuilt
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Also added index testing API (moved from main.c to index.c)
2017-07-19 10:25:11 -04:00
4aff301ef4
r190: default -k to 15; added -x map-ont
2017-07-19 10:11:14 -04:00
470021fd27
r189: sync with ksw2 (no effective changes)
2017-07-19 09:28:25 -04:00
71c988f6ab
r188: renamed bseq* to mm_bseq*
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to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
2017-07-19 09:26:46 -04:00
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
947cf162be
update dependency; delete minimap2-lite on clean
2017-07-18 14:48:46 -04:00
293a7049f3
migrated minimap/example.c here.
2017-07-18 14:43:43 -04:00
a1addb2949
use -msse4 by default, not -march
2017-07-18 13:56:51 -04:00
b4edb0cf55
fixed URL
2017-07-18 13:26:51 -04:00
9a935dcef5
Fixed grammar errors
2017-07-18 11:37:58 -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
f42790398d
fixed a band boundary bug in ksw2
2017-07-16 17:52:57 -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
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
Heng Li