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Author SHA1 Message Date
Heng Li e8d00a8c8c removed trailing ^M 2017-08-03 17:20:43 -04:00
Heng Li ed4efd77bc minor modifications 
I will submit this version arXiv. There is definitely room for improvement, but
as a semi-formal technical report, it should be good for now.
 2017-08-03 12:47:36 -04:00
Heng Li 295874ea30 spell check 2017-08-03 12:17:58 -04:00
Heng Li 9ec5f51afb the first draft 2017-08-03 12:12:55 -04:00
Heng Li 28ab4d1f72 backup 2017-08-02 22:59:58 -04:00
Heng Li 6c9390b54a backup 2017-08-02 19:52:31 -04:00
Heng Li 9306299e4d added benchmark results 2017-08-01 15:12:49 -04:00
Heng Li 0c563e1868 Merge branch 'dev' into tex 2017-08-01 13:53:16 -04:00
Heng Li 8b1e36c609 minor tweaks to the evaluation script 2017-08-01 13:52:29 -04:00
Heng Li d933a263d7 backup 2017-08-01 13:29:02 -04:00
Heng Li 7542b4b40a Makefile for TeX 2017-08-01 10:42:33 -04:00
Heng Li d6181de844 added tech notes 2017-08-01 10:38:33 -04:00
Heng Li 46de0fbdad Merge pull request #8 from rikuu/master 
fix self-comparison in index parameter override check
 2017-07-30 15:10:29 -04:00
Heng Li d8d4d29b68 Release minimap2-2.0rc1-r232 2017-07-30 14:32:40 -04:00
Heng Li e51dfd0330 added NEWS 2017-07-30 14:20:03 -04:00
Heng Li 1f78e1ee53 r230: code formatting changes only 2017-07-30 12:31:40 -04:00
Heng Li 5934d68772 r229: a new way to prevent out-of-band backtrack 2017-07-29 23:52:30 -04:00
Heng Li fa99d28d34 r228: reduced unnecessary INV alignment 2017-07-29 20:21:53 -04:00
Heng Li d08b7a0c51 r227: use local alignment for INV alignment 2017-07-29 17:40:53 -04:00
Heng Li da3db3c095 r226: only try inv alignment for primary 2017-07-29 14:09:35 -04:00
Heng Li 783ead6f47 r225: removed a debugging line 2017-07-29 13:21:38 -04:00
Heng Li 19d6ec885e r224: inversion alignment around Z-drop break 2017-07-29 13:09:10 -04:00
Heng Li 120bebc290 ake 2017-07-29 11:01:49 -04:00
Heng Li 5e3eecd6d4 r222: no effective changes 2017-07-29 10:31:46 -04:00
Heng Li 2179e9e24b r221: output SA in the SAM output 2017-07-28 23:08:39 -04:00
Heng Li 84922cfe41 clarify that wrong seeding mainly occurs in LCRs 2017-07-28 14:33:15 -04:00
Heng Li ebbe9c1eb8 r219: fixed a bug caused by skipping tandem seeds 2017-07-28 14:06:56 -04:00
Heng Li c672690564 r218: increase the frequency of SW slightly 2017-07-28 13:30:42 -04:00
Heng Li f4fee60188 r217: ignore tandem seeds during alignment 
This helps a tiny bit.
 2017-07-28 12:26:56 -04:00
Heng Li 254280b8af r216: a bit cleanup; identical output to r215 2017-07-28 11:54:18 -04:00
Heng Li fc965805f7 r215: bring back a log gap component 
Otherwise chaining may more often break a long gap into several gaps.
 2017-07-28 00:17:19 -04:00
Heng Li 667b32a516 added algorithm overview 2017-07-27 18:50:39 -04:00
Heng Li 2c79580649 r213: more careful solution to wrong seeds 
a little better, but not good enough!
 2017-07-27 13:19:11 -04:00
Heng Li b927838495 r212: better heuristic to fix wrong seeding 
but not good enough. Will explore more.
 2017-07-27 11:24:51 -04:00
Heng Li 371e20cc7c r211: a better heurstic to reduce false seeds 2017-07-26 23:56:38 -04:00
Heng Li 8b08a2ec41 added first-only and all-primary modes to eval 2017-07-26 19:32:26 -04:00
Heng Li 9f728dd96a tunable overlap ratio 2017-07-26 18:30:29 -04:00
Heng Li 323293fbda changed the way mapq is counted 2017-07-26 14:20:31 -04:00
Heng Li bd33bed455 make output better 2017-07-26 12:03:42 -04:00
Heng Li a01d758af6 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.
 2017-07-26 11:50:04 -04:00
Heng Li e9dc1ce2b6 r205: when computing mapq, consider min_chain_sc 
Not doing this was a mistake.
 2017-07-26 11:34:14 -04:00
Heng Li a8ad53ee81 evaluating read mapping for pbsim2fa reads 
More functionality to be added later
 2017-07-26 11:17:34 -04:00
Heng Li 00c6db5073 r203: check more subopt aln if score small 2017-07-25 20:02:44 -04:00
Heng Li f2ef48878a r202: trim bad chain ends before extension 
This fixes a few more FP long INDELs towards the end of alignments.
 2017-07-25 19:53:19 -04:00
Heng Li 21ca564112 r201: fixed a minor chaining issue 
Chaining looked at the end of a chain, but the end may not be the best. We now
go back to find the max.
 2017-07-25 18:26:51 -04:00
Heng Li 215e92ed7b r200: reduce long gaps in chaining 
Every seed can initiate a chain.
 2017-07-25 17:32:54 -04:00
Heng Li b530ade333 r199: changed to linear gap cost for chaining 
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
Heng Li 4bd7ebc39c convert pbsim .maf to fasta 2017-07-25 13:54:58 -04:00
Heng Li f81f37fef1 r197: allocate index seq names from kalloc 
to reduce malloc() overhead.
 2017-07-24 19:36:05 -04:00
Heng Li 5c4d040b13 r191: warning if CLI index opt diff from prebuilt 
Also added index testing API (moved from main.c to index.c)
 2017-07-19 10:25:11 -04:00
Heng Li 4aff301ef4 r190: default -k to 15; added -x map-ont 2017-07-19 10:11:14 -04:00
Heng Li 470021fd27 r189: sync with ksw2 (no effective changes) 2017-07-19 09:28:25 -04:00
Heng Li 71c988f6ab r188: renamed bseq* to mm_bseq* 
to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
 2017-07-19 09:26:46 -04:00
Heng Li b9b0b6f49c r187: fixed non-terminated sam output (#3) 
Only happen to unmapped read, with quality, and in the SAM output
 2017-07-18 15:20:29 -04:00
Heng Li 947cf162be update dependency; delete minimap2-lite on clean 2017-07-18 14:48:46 -04:00
Heng Li 293a7049f3 migrated minimap/example.c here. 2017-07-18 14:43:43 -04:00
Heng Li a1addb2949 use -msse4 by default, not -march 2017-07-18 13:56:51 -04:00
Heng Li b4edb0cf55 fixed URL 2017-07-18 13:26:51 -04:00
Heng Li 9a935dcef5 Fixed grammar errors 2017-07-18 11:37:58 -04:00
Heng Li 495a78e40a Get documentation ready for release 2017-07-18 11:04:09 -04:00
Heng Li 71e2a97a4c r180: changed -x asm5 settings 2017-07-18 00:00:36 -04:00
Heng Li 941059292e r179: changed the preset for assembly alignment 2017-07-17 22:41:46 -04:00
Heng Li 38aa66fa30 r178: fixed integer overflow in mapq calculation 2017-07-16 21:45:39 -04:00
Heng Li f42790398d fixed a band boundary bug in ksw2 2017-07-16 17:52:57 -04:00
Heng Li b4280d186f r176: removed seedcov_ratio; changed default opt 
min_seedcov_ratio is not used
 2017-07-12 12:47:46 -04:00
Heng Li 52caf79395 r175: halved max-chain-skip in the ava mode 2017-07-12 10:42:19 -04:00
Heng Li eeeb2ffb68 r174: make max-chain-skip work 
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
Heng Li 33451aba45 r173: changed the debugging output format 2017-07-11 15:23:28 -04:00
Heng Li cfa083a98b r172: separated PacBio and ONT read overlapping 
HPC k-mer works better for PacBio, but worse for ONT. Interesting...
 2017-07-11 15:12:35 -04:00
Heng Li 7598809577 r171: reduced log gap cost at chaining 
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
Heng Li 826c8ba892 r170: added a debugging flag 
something wrong with chaining
 2017-07-11 14:47:35 -04:00
Heng Li 801bc84b01 r169: output more accurate col. 10&11 to PAF 
In r168, col.10 is smaller than what it should be. This confuses miniasm.
 2017-07-11 14:09:51 -04:00
Heng Li 782449975d r168: fixed a bug in long join: a[] not sorted 
Also added length requirement for long join and changed -g in the ava mode
 2017-07-09 12:14:20 -04:00
Heng Li 1ac48556ae r167: long join threshold depends on gap 
also caught a bug for reverse strand join
 2017-07-09 10:38:51 -04:00
Heng Li 34ed85d46a optionally print the postions of long indels 2017-07-08 20:16:25 -04:00
Heng Li 2f11a63b22 script to collect alignment stats 2017-07-08 20:01:36 -04:00
Heng Li 4ee3202539 r164: unmapped read not properly flagged 2017-07-08 18:16:18 -04:00
Heng Li 42846ce65d r163: reduced long join score requirement 
because the chaining score is generally smaller with the last few commits.
 2017-07-08 15:51:52 -04:00
Heng Li 3f6a0b0b5c r162: improved chaining accuracy 2017-07-08 14:29:36 -04:00
Heng Li 38b2830e18 r161: filter bad seeds; changed default -g/-r 2017-07-08 13:31:27 -04:00
Heng Li 1fee5f8edc r160: -O and -E accept two numbers 2017-07-08 11:34:52 -04:00
Heng Li cc554aee43 r159: use two-piece gap penalty 2017-07-08 10:26:00 -04:00
Heng Li 9823317e8f r158: optionally ignore base quality 2017-07-05 18:23:50 -04:00
Heng Li d1f518e3ca for clarity 2017-07-04 11:56:50 -04:00
Heng Li 6b584a1235 added README 2017-07-04 11:47:29 -04:00
Heng Li 8fff901e53 added test data 2017-07-04 10:56:48 -04:00
Heng Li a65e557a7c Merge branch 'dev' 2017-07-03 13:19:17 -04:00
Heng Li e07daad7ad r153: sam primary record not set sometimes 2017-07-03 13:18:57 -04:00
Heng Li 6ead8af104 Merge branch 'dev' into 'master' 
Fixed bugs when reporting secondary alignments

See merge request !1
 2017-07-03 16:17:08 +00:00
Heng Li a94bc31311 r151: documentations 2017-07-03 12:11:07 -04:00
Heng Li b625247300 r150: mm_sync_regs() doesn't work with negative id 2017-07-03 11:36:34 -04:00
Heng Li 53c4bf5e4f r149: introduced debugging flags on CLI 2017-07-03 11:02:32 -04:00
Heng Li 2e4fd9f1d0 r148: revamped regs handling after cigar 2017-07-03 10:44:26 -04:00
Heng Li 696ebce66e backup; still buggy 2017-07-03 00:52:00 -04:00
Heng Li e06c342659 r146: in filtering, drop children if parent out 
This has been causing several segfaults.
 2017-07-03 00:28:12 -04:00
Heng Li 51cfb60520 r145: changed default -p from 2 to 0.8 
For long reads, secondary alignments can be very information.
 2017-07-02 22:51:45 -04:00
Heng Li 632b8638d2 r144: adjust primary aln after cigar 2017-07-02 22:43:02 -04:00
Heng Li 2b45ba7a0b r143: fixed a segfault and incorrect .parent 2017-07-02 19:56:21 -04:00
Heng Li 74d306a596 fixed bug when retaining 2ndary aln; still buggy 2017-07-02 19:08:30 -04:00
Heng Li da90b614db r141: replaced -b with -a (for SAM output) 
-b sounds like BAM. I like -a better.
 2017-07-01 16:54:59 -04:00