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Author SHA1 Message Date
Heng Li 1b1dd0cd57 r442: default max_gap to 200 in the sr mode 2017-09-26 13:31:01 -04:00
Heng Li 92ec8bd859 added the /1 or /2 suffix 2017-09-26 12:04:35 -04:00
Heng Li 55d1e4f638 r440: better chain filtering for PE reads 2017-09-26 11:03:36 -04:00
Heng Li 64c0ad6b35 r439: use splice-like chain gap cost between segs 
This improves accuracy
 2017-09-25 16:04:38 -04:00
Heng Li 9538c985aa r438: fixed a rare case that leads to missing hits 
It is a bug in chaining.
 2017-09-25 14:59:34 -04:00
Heng Li 8f25cfa36e r437: fixed uninialized memory on rep_len 2017-09-25 14:22:45 -04:00
Heng Li 81008dd371 r436: working on short reads 
The result is mixed - lots of room for tuning
 2017-09-25 14:06:29 -04:00
Heng Li 3bb66e1ed3 multi-seg working on toy examples 2017-09-25 13:42:04 -04:00
Heng Li a742f10164 get multi-seg code ready; probably not working yet 2017-09-24 15:17:17 -04:00
Heng Li f0951141a1 allow to read multiple files interleaved 2017-09-24 14:33:05 -04:00
Heng Li 84bbc47152 two arrays should be freed with kfree(0,) 
though in the current code, they are strictly equivalent.
 2017-09-23 10:43:22 -04:00
Heng Li 5400191097 get batch sequence reader ready for paired-end 2017-09-22 09:56:31 -04:00
Heng Li ef84e8b4e7 Merge branch 'master' into sr 2017-09-20 23:56:06 -04:00
Heng Li 1c948e0d1d added GMAP iso-seq numbers 2017-09-20 23:54:02 -04:00
Heng Li 997011458c fixed uninitialized value due to last commit 2017-09-20 15:10:48 -04:00
Heng Li 19d8eca3a1 moved array shrinking into chain_dp() 2017-09-20 14:58:57 -04:00
Heng Li 9943e5fdd0 backup 2017-09-20 14:35:46 -04:00
Heng Li 5b39a1b34b Merge branch 'master' into sr 2017-09-20 12:24:08 -04:00
Heng Li e3b5802b2e r424: reduce memory for long query seqs 2017-09-20 12:22:13 -04:00
Heng Li 03d6894517 backup 2017-09-20 11:47:46 -04:00
Heng Li 645db3350e Merge branch 'master' into sr 2017-09-20 11:15:14 -04:00
Heng Li 75e6bbc9f6 r421: removed the MM_F_SPLICE_BOTH mode 
In the default splice mode, minimap2 applies two rounds of spliced alignment:
first assuming GT-AG to be the splice signal across all splicing sites and then
assuming CT-AC to be the signal. This is the idea strategy.

In the MM_F_SPLICE_BOTH mode, minimap2 applies one round of spliced alignment,
assuming GT-AG and CT-AC to be the splice signals AT THE SAME TIME. This will
be faster but less accurate. I don't think anyone would like to run minimap2 in
this mode, so I am removing it for clarity.
 2017-09-20 11:11:53 -04:00
Heng Li 7a9b4db874 replaced --approx-ext with --sr 
--sr disables Z-drop and may come with other heurstics
 2017-09-20 10:51:18 -04:00
Heng Li 4979e66ff0 Merge branch 'master' into sr 2017-09-20 10:20:31 -04:00
Heng Li a686461e83 added github downloads counts 2017-09-20 10:11:58 -04:00
Heng Li fd14618e61 no effective changes 2017-09-20 10:11:05 -04:00
Heng Li 5caadc28b4 Merge branch 'master' into sr 2017-09-19 22:31:14 -04:00
Heng Li 56014ba3db avoid assertion failure given 0-length reads 2017-09-19 22:30:32 -04:00
Heng Li b99c22840f r414: avoid assertion failure for 0-length reads 2017-09-19 22:21:27 -04:00
Heng Li c04420698e fixed an uninitialized value 2017-09-19 16:21:21 -04:00
Heng Li fb1bcc0084 early exploration 2017-09-19 16:18:28 -04:00
Heng Li 11081c6c27 r411: refactored kalloc for clarity 
The new version is closer to K&R's original implementation.
 2017-09-18 19:49:15 -04:00
Heng Li 60485790b4 updated version number in README 2017-09-17 20:25:54 -04:00
Heng Li ea5a0cd17d Release minimap2-2.2 (r409) 2017-09-17 20:08:47 -04:00
Heng Li ffff953e2c added python version badge 2017-09-17 17:15:55 -04:00
Heng Li 48705e9bfa don't build for python-3.0 (unavailable in travis) 2017-09-17 17:07:42 -04:00
Heng Li cf93e5c0a1 more functional minimap2.py; added categories 2017-09-17 17:06:39 -04:00
Heng Li 0b660c70e2 syntax error 2017-09-17 16:02:06 -04:00
Heng Li 5715c423ff exposed timer and verbose-level to mappy 2017-09-17 15:21:36 -04:00
Heng Li c8a019fae8 exposed fasta/q reader to mappy 2017-09-17 14:41:59 -04:00
Heng Li e9c57f6d8b r402: exposed kseq (for API in mappy later) 2017-09-17 13:09:16 -04:00
Heng Li 3edf2a9130 renamed mm2-lite.py to minimap2.py 2017-09-17 09:41:37 -04:00
Heng Li 89151b2588 added python 3.6 test 2017-09-17 00:55:31 -04:00
Heng Li cc0a538bd3 try python3 in travis 2017-09-17 00:49:16 -04:00
Heng Li e9e86f5a48 try python build again 2017-09-17 00:46:39 -04:00
Heng Li c0779f0359 revert to the old travis 
can't get cython working...
 2017-09-17 00:40:18 -04:00
Heng Li 875ea06302 install cython with travis 2017-09-17 00:37:09 -04:00
Heng Li 2c7007a11b try again 2017-09-17 00:31:15 -04:00
Heng Li fc87b767ba travis for python (test) 2017-09-17 00:28:34 -04:00
Heng Li dba8b50ee9 change python version to rc1 2017-09-17 00:08:54 -04:00
Heng Li d5012a1b17 this is embarrassing: rename again to mappy 2017-09-17 00:05:30 -04:00
Heng Li eaaf53c9b8 bumped version number 
due to conflict with PyPI (already uploaded)
 2017-09-16 23:51:49 -04:00
Heng Li ef46a8aed4 remaining minimap2=>mmappy in doc 2017-09-16 23:49:02 -04:00
Heng Li 28fd3d63fd renamed module name from minimap2 to mmappy 
minimap2 clashed with minimap2 from conda
 2017-09-16 23:29:41 -04:00
Heng Li 06b79c4a52 Merge branch 'master' of github.com:lh3/minimap2 2017-09-16 22:53:34 -04:00
Heng Li 8cdaae0935 fixed a few typos 
eh... a missing fix
 2017-09-16 22:53:24 -04:00
Heng Li 38aa9aa9a7 eh... a missing fix 2017-09-16 22:52:52 -04:00
Heng Li f8cb865ec5 fixed a few typos 2017-09-16 22:52:26 -04:00
Heng Li 1d90742b35 fixed hyperlink 2017-09-16 22:46:30 -04:00
Heng Li 5103cea7d3 load python README.rst into setup.py 2017-09-16 22:43:52 -04:00
Heng Li 7da9a08a6f reformat 2017-09-16 22:36:19 -04:00
Heng Li ddc2c6f279 change to rst for PyPI 2017-09-16 22:29:52 -04:00
Heng Li 7e98b18ba2 for python3 compatibility 2017-09-16 20:37:49 -04:00
Heng Li 3544c60c71 allow to test if index is present 2017-09-16 20:09:17 -04:00
Heng Li 6b66ec6167 minor 2017-09-16 19:55:33 -04:00
Heng Li cb7fb77bb9 python documentation 2017-09-16 19:50:52 -04:00
Heng Li 322e5a16e5 minor tweaks to python 2017-09-16 18:11:43 -04:00
Heng Li 10bd4079d1 fixed a bug on rev strand; added example 2017-09-16 17:51:13 -04:00
Heng Li b22703a354 improvement to the python binding 2017-09-16 11:14:01 -04:00
Heng Li 7e34bea7ab minor 2017-09-16 09:30:00 -04:00
Heng Li c07f9f9a49 r372: default mm_verbose to 1, and change in main 2017-09-16 09:14:34 -04:00
Heng Li 446bde214d first python version 2017-09-16 08:44:47 -04:00
Heng Li 5966e5d6e4 make reader_open() work even if idxopt is NULL 2017-09-15 11:29:49 -04:00
Heng Li 14b853499f r369: updated example with the latest API 2017-09-14 22:44:10 -04:00
Heng Li 75ff7ceec5 r368: API documentation 2017-09-14 22:23:04 -04:00
Heng Li e2823d4aee r367: index reader optionally writes index 2017-09-14 21:18:13 -04:00
Heng Li eb00521d9b redesigned indexing and option APIs 2017-09-14 17:02:01 -04:00
Heng Li 0f7455cefa r365: documented the "sr" preset 2017-09-14 12:57:21 -04:00
Heng Li 4d3768bf26 r364: improved the mapq heuristics 
* use repetitive seed lengths, not counts
* compute n_sub to higher accuracy
* use bwa-mem mapq heuristic as a backup

For short single-end reads, minimap2's ROC is not as good as bwa-mem's, but is
close.
 2017-09-14 12:37:03 -04:00
Heng Li 47e9d76ca1 further mapq tuning 2017-09-14 10:46:14 -04:00
Heng Li f4a8766283 r362: fixed overestimated chaining score 
Caused by ilog2_32(0)=-1. This bug was fixed once and reoccurred as I was
tuning the score function but forgot to apply the fix.
 2017-09-14 10:15:22 -04:00
Heng Li 6a82a21dee r361: improved mapq for short reads 2017-09-13 15:32:39 -04:00
Heng Li 3c91d652dd r360: allow to set integer max occ 2017-09-13 11:37:00 -04:00
Heng Li 1b44275802 Merge branch 'master' into sr 2017-09-13 11:10:23 -04:00
Heng Li 2f2b11624a reverted to the Travis badge as it is faster 2017-09-13 10:50:03 -04:00
Heng Li cb57bd6146 updated badges 2017-09-13 10:46:25 -04:00
Heng Li 885db1233d updated badges 
for fun
 2017-09-13 10:29:41 -04:00
Heng Li 2bf2f137dd added a license badge 2017-09-13 10:03:15 -04:00
Heng Li 8706f6bdf8 Merge branch 'master' into sr 2017-09-12 22:37:46 -04:00
Heng Li 2028e8c266 show bioconda version 2017-09-12 16:21:49 -04:00
Heng Li 0cc8d277ba changed to the "install with conda" badge 2017-09-12 16:20:01 -04:00
Heng Li 14f0cce4e2 malformatted conda badge 2017-09-12 16:17:07 -04:00
Heng Li 8ddbf7169f added bioconda download link 2017-09-12 16:16:26 -04:00
Heng Li d7f2ac1d4f better parameters for short reads 
It turns out the key problem is not the minimizer density. It is the max
occurrence that tends to affect results more, especially sensitivity. There is
still lots of work to do, but for now, it seems a good start.
 2017-09-12 16:11:23 -04:00
Heng Li eea9e851d8 Merge branch 'dev' into short 2017-09-11 09:32:28 -04:00
Heng Li c7c3585531 r347: merged mm_map_frag() into mm_map() 
mm_map_frag() was separated due to an earlier design that has been rejected.
 2017-09-10 15:02:55 -04:00
Heng Li 87a278d06a Merge branch 'dev' into short 2017-09-09 08:49:58 -04:00
Heng Li 59c822b722 removed some commented code 
which *might* return at some time later
 2017-09-09 08:38:39 -04:00
Heng Li f422175e4e r344: avoid unnecessary refName retrieval 2017-09-08 22:44:14 -04:00
Heng Li 709b6ec1f1 increase seed occurrences 2017-09-08 22:42:39 -04:00