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Author SHA1 Message Date
Heng Li e9607fcd9b allow to convert read names 
ONT read names are just too long and too hard to compress
 2018-01-05 22:05:15 -05:00
Heng Li a465a920ec bug in block starts; added color and short-name 2018-01-05 21:45:56 -05:00
Heng Li b20839be77 more robust ID conversion 2018-01-05 17:55:24 -05:00
Heng Li 209beb9955 convert EnsEMBL to UCSC name (optional) 2018-01-05 17:41:18 -05:00
Heng Li cfe87f50c1 convert GTF/GFF3 to BED12 2018-01-05 17:10:43 -05:00
Heng Li 680b971bb0 deleted duplicated entries 2018-01-01 19:52:21 -05:00
Heng Li 6b0d3c1fa8 added PHONY and comments to makefile 2017-12-30 20:54:11 -05:00
Heng Li dc9e3dcf4a r639: changed -O/-E validation 2017-12-30 20:39:29 -05:00
Heng Li cc75c12905 r638: disabled scoring checking 
I haven't figured out the exact bounds...
 2017-12-30 07:50:40 -05:00
Heng Li f159e1c2d3 new section on HPC k-mers 2017-12-24 19:11:23 -05:00
Heng Li 3a375d3436 renamed paf2ovlp to ov-eval 2017-12-24 18:04:00 -05:00
Heng Li 626f10e0d0 evaluate sensitivity in the same script 2017-12-24 17:55:42 -05:00
Heng Li b997578078 find reads overlaps based on reference alignment 2017-12-24 17:20:27 -05:00
Heng Li ce8a48d715 fixed two minor typos in references 2017-12-24 13:14:47 -05:00
Heng Li 99879e9e75 a new section on estimating sequence divergence 2017-12-24 12:57:38 -05:00
Heng Li c969d1a1ce updated direct RNA-seq results; cite syndip 
and a few minor changes
 2017-12-24 11:06:17 -05:00
Heng Li fcac296c4a clarify ARM-NEON support in README 2017-12-18 23:01:44 -05:00
Heng Li e420b17496 r629: API to construct index from strings 2017-12-18 22:29:46 -05:00
Heng Li 23a846c594 Merge pull request #81 from hasindu2008/master 
minimap2 on ARM processors
 2017-12-16 09:40:41 -05:00
Heng Li ab345e600b r626: function to check incorrect scoring system 2017-12-13 12:23:43 -05:00
Heng Li d003a00d71 r625: HPC sketch still has one minor issue 2017-12-13 09:40:42 -05:00
Heng Li ae85dcde76 added esterr.o dependencies 2017-12-13 09:01:48 -05:00
Heng Li eb819c29e8 Release minimap2-2.6 (r623) 2017-12-12 11:09:59 -05:00
Heng Li fb630de40a r622: fixed bug in sdust due to recent refactor 2017-12-11 15:32:28 -05:00
Heng Li 43960a8ca7 r621: --print-qname also shows kalloc status 2017-12-11 12:30:08 -05:00
Heng Li f6608fe99c r620: revamped thread-local memory management 
* Don't preallocate sdust_buf or minizer list. kalloc should be fast enough -
  benchmarks needed to confirm.

* Fixed a memory leak caused by divergence estimate (post v2.5)

* Reset the kalloc buffer after mapping a long query. This reduces peak memory
  when large chunks of memory are allocated, at the cost of performance, though.
 2017-12-11 12:11:10 -05:00
Heng Li 98a6e52c06 r618: heuristics to avoid tiny terminal exons 2017-12-11 00:57:55 -05:00
Heng Li 824712a4ee r617: removed some unused code 2017-12-10 17:54:50 -05:00
Heng Li 0e42628ef6 r611: document --idx-no-seq; better inv aln 2017-12-08 13:16:18 -05:00
Heng Li 98a999fe44 r611: added pseudocount when est divergence 2017-12-08 12:57:57 -05:00
Heng Li fec7bd713f r610: warning if db sequence is 0-lengthed (#69) 2017-12-07 21:05:39 -05:00
Heng Li 2f693e8ca4 r609: bugfix - SDUST masking not working 2017-12-07 11:45:38 -05:00
Heng Li 704ff9f4c6 r607: estimate sequence divergence 
Currently using the simplest method. There may be a more accurate estimate.
 2017-12-06 16:14:39 -05:00
Heng Li 68c63f2d68 r606: fixed a sketch bug for long 256bp k-mer 
sketch() writes {-1,-1} to the output array.
 2017-12-06 16:13:29 -05:00
Heng Li 76206f574f support both SAM and PAF as input 2017-12-02 21:57:19 -05:00
Heng Li e575f884e1 convert spliced PAF to BED 2017-12-02 21:23:41 -05:00
Heng Li 571161d5a2 changed badges 2017-12-01 16:16:27 -05:00
Heng Li 07d41efc2b explain secondary/supplementary aln for RNA-seq 2017-11-30 23:02:20 -05:00
Heng Li 984f7846c0 r601: bugfix - a similar issue to r600 
This bug unsets the alignment score of suboptimal alignments.
 2017-11-30 11:51:34 -05:00
Heng Li af1d6afba9 r600: bugfix - missing secondary alignments (#71) 
This should very rarely happen to typical data, but has a higher chance in
artifactual data.
 2017-11-30 11:34:10 -05:00
Heng Li cbdb6c069f when there are incorrect anno, warn but not abort 2017-11-24 12:48:49 -05:00
Heng Li 35b6d9f7d5 direct manpage to HTML 2017-11-24 11:05:20 -05:00
Heng Li 39a9666246 convert PAF to LAST's cigar output 
also added the support of BLAST-like output for "--cs=short".
 2017-11-18 20:30:44 -05:00
Heng Li 662d05dc02 fixed incorrect var coordinate 2017-11-12 20:25:33 -05:00
Heng Li 379457c18b use mapq threshold 2017-11-12 19:01:34 -05:00
Heng Li 03169d590b print cov-1 regions (not BED output any more) 2017-11-12 18:45:49 -05:00
Heng Li 8c8d446820 find regions covered by one contig 2017-11-12 18:41:01 -05:00
Heng Li 0ddb064f17 dnadiff-like script; improvement coming 2017-11-12 15:07:29 -05:00
Heng Li 131cfc6938 r574: build index without sequences 2017-11-11 21:38:38 -05:00
Heng Li 2f463b1db0 r573: prepare to generalize index 2017-11-11 19:54:06 -05:00
Heng Li 3b518271ee Release minimap2-2.5 (r572) 2017-11-11 11:29:28 -05:00
Heng Li 481d8239e9 Merge pull request #57 from cjw85/strand_typo 
Fix typo in strand property
 2017-11-10 20:36:19 -05:00
Heng Li d7a31e40e6 r569: last commit is buggy 2017-11-09 23:20:41 -05:00
Heng Li dd18cd75de r568: revert - don't take max(dp_max, dp_score) 2017-11-09 23:12:48 -05:00
Heng Li 99a2709913 r567: minor change to #56 2017-11-09 19:17:45 -05:00
Heng Li 032068a747 Merge pull request #56 from mvdbeek/softclipping 
Implement -Y for soft clipping of supp. alignments
 2017-11-09 19:12:47 -05:00
Heng Li 422b43374e Merge pull request #55 from martinghunt/fix_python3_strings 
Bug fix with byte strings in Python3
 2017-11-09 09:37:41 -05:00
Heng Li a7b38f6900 r562: fixed a severe bug: wrong query start 2017-11-08 22:31:05 -05:00
Heng Li e896c9ec05 r559: prefer a chain involving more segments 2017-11-08 13:22:16 -05:00
Heng Li 98ba8928c6 r558: dp_max no less than dp_score 2017-11-08 10:06:10 -05:00
Heng Li bcf8462d20 Merge pull request #52 from cvdelannoy/patch-1 
Update README.md
 2017-11-08 07:50:31 -05:00
Heng Li b24d68ae9f r557: fixed another mapq underestimate 
When a chain is split during base-level alignment, its chaining score is
reduced. However, the chaining score of its suboptimal chain remains the same.
This leads to underestimated mapping quality.
 2017-11-07 23:20:49 -05:00
Heng Li 65deedfa96 r556: bugfix - underestimate mapq for split aln 2017-11-07 22:37:12 -05:00
Heng Li 21a46ba652 Release minimap2-2.4 (r555) 2017-11-06 12:54:02 -05:00
Heng Li 1617b87ee1 this will become version 3 at arXiv 2017-11-06 10:57:12 -05:00
Heng Li 2191ac58ad two discussion paragraphs; need one more 2017-11-05 12:27:52 -05:00
Heng Li fa5a645ca5 r552: fixed a tiny typo on struct packing 
The old packing wastes memory, thought very small.
 2017-11-05 08:27:26 -05:00
Heng Li c2b09356b8 moved conclusion to result; need new discussion 2017-11-04 22:19:46 -04:00
Heng Li a3f0aa1d5b r550: fixed -L issues with secondary and supp aln 2017-11-04 12:13:38 -04:00
Heng Li 52ffbc9e0c added bowtie2 and snap versions 2017-11-02 15:51:23 -04:00
Heng Li a9790c0f1d added two bowtie2 numbers for comparison 2017-11-02 15:44:48 -04:00
Heng Li d0ac78ac08 updated the tech note 2017-11-02 15:37:24 -04:00
Heng Li 22290db3e4 r546: minor mapQ tuning 2017-11-01 13:20:39 -04:00
Heng Li cd24dc8834 r545: removed option -i, not working well 2017-10-31 22:23:27 -04:00
Heng Li b8e758df0f r544: increased PE mapQ 2017-10-31 16:55:02 -04:00
Heng Li 311fa90030 r543: applied some sr mapq changes to long reads 2017-10-31 15:24:05 -04:00
Heng Li fb8a1b5536 r542: tuning mapQ calculation 2017-10-31 14:25:09 -04:00
Heng Li 7f11f4c4d4 Instructions on different long RNA-seq techs 2017-10-29 13:58:25 -04:00
Heng Li 285eb0da05 r540: removed a buggy debugging line 2017-10-29 00:02:41 -04:00
Heng Li 192217a10c r539: use --splice-flank=yes by default 
In human/mouse, the GTr..yAG pattern occurs to 91/92% of all GT-AG introns.
Modeling r..y clearly leads to higher accuracy. However, in SIRV, this
percentage is reduced to ~60%. The default "--splice --splice-flank=yes"
leads to lower accuracy. If someone benchmark minimap2 on SIRV, this would be
bad, but minimap2 is developed for practical applications, not for benchmarks.
I will live with that.
 2017-10-28 22:29:55 -04:00
Heng Li f22a94e868 r538: fixed a long existing bug in HPC k-mer (#47) 
This bug may lead to a wrong minimizer when a HPC k-mer is longer than 256bp.
When there is a seed match involving this wrong HPC k-mer, the correct seed
sequences do not match in fact. This violates the assumption in align.c and
subsequently causes a segfault, which is what #47 has caught. This bug lurked
in the earliest piece of code and affected all released minimap2 versions so
far. It is extremely rare and does not affect the prebuilt GRCh37/38 indices.
 2017-10-28 19:21:10 -04:00
Heng Li 79b0caca95 r537: model the next base to GT/AG 
[PMID:18688272] shows that the base following GT tends to be A or G (i.e. R) in
both human and yeast, and that the base preceeding AG tends to be C or T (i.e.
Y). In the new model, we pay no cost to GTr..yAG, but we pay half of the cost
if there is no r or y. This improves the junction accuracy when mapping to
human and mouse and decreases the accuacy when mapping to SIRV. My guess is
that SIRV does not honor this trend. Need to investigate in future.

Also in this commit, --cost-non-gt-ag is aliased to -C. The default is changed
to 9 instead of 5. I also added --splice-flank to enable the above model. This
may become the default once I confirm my hypothesis on SIRV.
 2017-10-28 00:25:01 -04:00
Heng Li afc2f2e84b r536: removed an unnecessary assert() 2017-10-24 21:08:54 -04:00
Heng Li e6f66f2f3b disabled download counts 
seems not working any more
 2017-10-24 14:40:08 -04:00
Heng Li 70735098e2 fixed a typo in README 2017-10-24 14:39:33 -04:00
Heng Li d4b5dfc297 r533: added --no-pairing 
to prevent the use of any pairing information for paired-end reads.
 2017-10-23 14:09:32 -04:00
Heng Li 5acd709524 updated the download link to v2.3 2017-10-23 13:43:31 -04:00
Heng Li 306e4541f8 Released minimap2-2.3 (r531) 2017-10-22 23:13:35 -04:00
Heng Li 1dd221ad82 a bit more on short read mapping 
The tech note still needs improvement. Will do that after the release of v2.3.
 2017-10-22 18:38:35 -04:00
Heng Li c6b6392b70 minor wording changes 2017-10-21 23:46:36 -04:00
Heng Li dc37aee881 minor wording changes 2017-10-21 23:38:05 -04:00
Heng Li 37e627aa98 note on long cigar in README 2017-10-21 22:28:06 -04:00
Heng Li beeb806829 r526: fixed a bug when HPC is in use 
It happened when the query HPC minimizer is longer than the reference HPC
minimizer close to the beginning of a contig. We may get a negative coordinate,
which causes an assertion failure.
 2017-10-21 19:54:04 -04:00
Heng Li be7f3c4ffe r525: fixed a bug in chaining; handle ovlp ends 2017-10-20 21:34:52 -04:00
Heng Li bd04372873 r524: reverted to bwa-mem end bonus 
and reduced the cost of clipping when filtering by identity
 2017-10-20 16:57:31 -04:00
Heng Li 15ed0712c2 r523: fixed a performance bug in ksw2_ll 
Wont' affect accuracy.
 2017-10-20 13:00:10 -04:00
Heng Li 55dcbefe87 updated text (unfinished) 2017-10-20 12:44:54 -04:00
Heng Li 8abba332ad replaced mapQ plot with sr roc 
figure legend and text to be updated later
 2017-10-19 23:43:17 -04:00
Heng Li 4683da2455 r520: added option -L to write long cigar to CG 2017-10-17 17:32:44 -04:00
Heng Li ffd953029f r519: fixed a severe bug that misses long alns 2017-10-17 15:52:36 -04:00