fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-07 22:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity
304 Commits 9 Branches 35 Tags
bf8246f8729e45be1f6a8d8cdcecb4979a67eb76
Commit Graph
100 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Heng Li bf8246f872 Release minimap2-2.1-r311 2017-08-25 13:35:55 +08:00
Heng Li 5cbd776651 test data for spliced alignment 2017-08-25 13:17:56 +08:00
Heng Li 0fe1a224ab r309: improved SAM header output 2017-08-25 10:35:58 +08:00
Heng Li 240f6caaff backup manuscript 2017-08-24 22:05:14 +08:00
Heng Li b8bdac7e64 backup 2017-08-22 17:45:01 +08:00
Heng Li 19e4b2aab0 backup 2017-08-20 22:10:03 +08:00
Heng Li ce859dbe1c evaluate introns 
this simplies the metrics
 2017-08-20 21:54:59 +08:00
Heng Li a4c41f64a5 the final version 
to be replaced by intron-eval
 2017-08-20 21:54:35 +08:00
Heng Li 5ed2faf270 minor tuning to the matching rules 2017-08-19 16:21:49 +08:00
Heng Li 8058c85b72 moved appendix to methods; detailed splice aln 2017-08-18 23:33:57 +08:00
Heng Li 993a2bb521 r301: separate introns from deletions 
When an intron is adjacent to a deletion, the old code count both as introns,
which lead to an inaccurate exon boundary.
 2017-08-18 15:31:15 +08:00
Heng Li 64c1389e1a Merge branch 'master' into splice 2017-08-17 23:39:27 +08:00
Heng Li 81cff97208 r299: support -h: output to stdout; return 0 2017-08-17 23:38:31 +08:00
Heng Li bbb37d95f2 support inserting RG lines 2017-08-17 23:34:09 +08:00
Heng Li 2cde8d257c r297: bidirectional RNA alignment 2017-08-17 06:02:44 -04:00
Heng Li b5f5929bf9 r296: expose splicing related options to CLI 2017-08-13 21:37:51 -04:00
Heng Li 28f86688ab r295: gap closure from the middle of non-HPC k 
This WILL slightly affect the result of genomic mapping, but hopefully
in the good direction.
 2017-08-12 23:48:43 -04:00
Heng Li 43506edbc5 backup: preliminary boundary alignment 2017-08-12 23:10:14 -04:00
Heng Li bcfe00d2ad minor formatting changes 2017-08-12 19:09:33 -04:00
Heng Li 17c19e5819 exts2 working 2017-08-12 19:06:59 -04:00
Heng Li 61eef0575c separate out spliced alignment; not right yet 2017-08-12 18:54:32 -04:00
Heng Li 53b3265d84 r290: in techrep, explain spliced alignment 2017-08-12 15:40:49 -04:00
Heng Li a23df2dc91 r289: changed CLI help only 2017-08-12 12:40:07 -04:00
Heng Li 5a74088b74 r288: changed max intron length to 200k 2017-08-12 12:39:21 -04:00
Heng Li d240318741 r287: refined CLI options and manpage 2017-08-12 12:26:04 -04:00
Heng Li 0f4c823b0c r286: ignore introns when computing max seg score 2017-08-12 10:58:16 -04:00
Heng Li 2d11aaa830 option to print all exons for debugging 2017-08-12 10:04:16 -04:00
Heng Li 30b8cb4672 option to print correct exons 2017-08-11 17:50:21 -04:00
Heng Li 0c1760bc86 bugfix; print errors; better rules 2017-08-11 16:28:52 -04:00
Heng Li a99358bc3d r282: reduced intron cost; added eval script 2017-08-11 00:06:01 -04:00
Heng Li 163fa36ee6 r281: don't open long gaps on query 2017-08-10 15:04:59 -04:00
Heng Li c59b0781bc r280: output introns as "N" in the cdna mode 2017-08-09 11:45:02 -04:00
Heng Li 7429b12164 Merge branch 'master' into cdna 2017-08-08 22:00:24 -04:00
Heng Li 9e1125edda r277: abort if query/-d missing (#11) 2017-08-08 21:46:15 -04:00
Heng Li 4db0d1034b Show travis CI status 2017-08-08 21:32:56 -04:00
Heng Li 3dbe23b34e Merge branch 'dev' 2017-08-08 21:30:32 -04:00
Heng Li 6840370f3c Release minimap2-2.0 (r275) 2017-08-08 21:16:25 -04:00
Heng Li 7f9f659b6a r274: CLI option to change max ref gap 2017-08-08 11:39:23 -04:00
Heng Li 1a7d782131 r273: cdna mapping mode for testing 
Differences from the typical mapping mode:

* banded alignment disabled
* log gap cost during chaining
* zero long-gap extension during alignment
* up to 100kb (by default) reference gap
* bad seeding not filtered (to tune later)
 2017-08-08 11:31:49 -04:00
Heng Li 4badf2fcbf avoid wasted memory allocation for backtrack 2017-08-08 11:29:46 -04:00
Heng Li 0137d0dfab command lines used for read simulation 2017-08-07 13:41:40 -04:00
Heng Li 5b10667967 sim-eval.js to support mason2 read names and SAM 2017-08-07 13:28:33 -04:00
Heng Li bd1541dce1 renamed simulation-related scripts 2017-08-07 13:26:25 -04:00
Heng Li 1597f2b030 convert mason2 SAM to fastq 2017-08-07 12:45:34 -04:00
Heng Li ce927d2aee Merge branch 'master' into dev 2017-08-07 12:44:07 -04:00
Heng Li 8c2917b391 Added citation. 2017-08-06 21:30:47 -04:00
Heng Li 9fcf8b6315 added basic travis CI 2017-08-04 15:33:40 -04:00
Heng Li 3217178d4a fixed k8 download page 2017-08-04 14:53:00 -04:00
Heng Li b40598fa91 added paf2aln.js example 2017-08-04 14:51:33 -04:00
Heng Li 269b8661b9 minor clarification 2017-08-04 14:49:25 -04:00
Heng Li 890d7bbd5b added README for misc scripts 2017-08-04 14:46:31 -04:00
Heng Li 1aca0d5098 copied sam2paf.js here for completeness 2017-08-04 14:44:37 -04:00
Heng Li 68d99f0edb Merge branch 'cs-tag' into dev 2017-08-04 14:31:46 -04:00
Heng Li fd66ab5413 blast-like output working 2017-08-04 14:31:21 -04:00
Heng Li 71f82759af convert paf to maf 2017-08-04 13:05:46 -04:00
Heng Li 648cdd8a3b minor wording changes 2017-08-04 10:21:10 -04:00
Heng Li 7e231cfd3a minor wording improvement 2017-08-03 21:28:01 -04:00
Heng Li 95d3c30ae3 rephrasing a bit to avoid the apparent TeX bug 
Several hours sank into this. Damned...
 2017-08-03 20:19:00 -04:00
Heng Li f57fd8c790 added one transition phrase 
as there are no subsubsections now
 2017-08-03 18:01:48 -04:00
Heng Li c70b20ee6d removed subsubsection 
TeX Live 2016 doesn't work with section and content on the same line.
 2017-08-03 17:58:36 -04:00
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 12cea727b8 r238: bugfix to cs - rev sequence not complemented 2017-08-01 10:33:21 -04:00
Heng Li cd105b47f2 r237: fixed a bug in outputting cs:Z 2017-07-31 14:49:39 -04:00
Heng Li 35f232c3fa r236: in cs tag, output differences in lowercase 
for easy eyeballing
 2017-07-31 12:17:48 -04:00
Heng Li 4c0713ee14 r235: optionally output tag cs in PAF 
cs encodes the query, the reference sequence and CIGAR.
 2017-07-31 12:06:49 -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