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Author SHA1 Message Date
Heng Li bf2d4f7aec r486: treat "U" as "T" for RNA reads (#33) 2017-10-07 18:53:25 -04:00
Heng Li 47b86e765b minor wording changes 2017-10-06 15:34:20 -04:00
Heng Li 56acf6ee28 completed README rewrite 2017-10-06 14:26:02 -04:00
Heng Li 4f6244bd4a revamped README; not finished yet 2017-10-06 13:02:25 -04:00
Heng Li c6384ed2c8 r482: increased short-read bandwidth to 100 
This has very minor effect on speed.
 2017-10-06 10:20:32 -04:00
Heng Li 2833a9c255 150bp mason2 simulation 2017-10-06 09:46:59 -04:00
Heng Li de2fcc1bf3 updated the mappy 2017-10-05 17:10:07 -04:00
Heng Li e0baf1ad54 r479: a bit code cleanup 2017-10-05 16:15:14 -04:00
Heng Li f266092699 r478: simplied useless code, a tiny bit 2017-10-05 15:56:00 -04:00
Heng Li 9c5767f9ed r477: renamed multi_seg to frag_mode 2017-10-05 15:48:17 -04:00
Heng Li ae2adf04d4 r476: multi-file fragment mode working 2017-10-05 15:39:26 -04:00
Heng Li b839758335 r475: added --cs=none; updated manpage 2017-10-05 15:27:37 -04:00
Heng Li f4a5d3a692 r474: replaced -S and --cs-no-equal with --cs 2017-10-05 15:03:03 -04:00
Heng Li 3ff6eda3a4 r473: don't count introns into blen 2017-10-05 14:37:21 -04:00
Heng Li 1a90bc8603 r472: fixed a bug when printing MAPQ/CIGAR 2017-10-05 12:46:11 -04:00
Heng Li abf2a90363 r471: all SAM features implemented; more tests! 2017-10-05 12:37:30 -04:00
Heng Li 5ab99eb26e more accurate SAM flag 2017-10-05 10:59:38 -04:00
Heng Li 7cc4f6f965 r469: first step towards PE SAM 2017-10-05 10:38:09 -04:00
Heng Li 16e6e589a8 r468: replaced ^ with ~ in cs 2017-10-04 22:17:12 -04:00
Heng Li 9aba11769c r467: added : (equal length) and ^ (intron) ops 2017-10-04 21:55:37 -04:00
Heng Li 7d50e646dd r466: detect multi-part index more smartly 
though it might not work in an extremely rare case: the end of a sequence ends
at X*16384 and it is the last sequence in a batch. This can be resolved by
never letting the kstream_t buffer empty.
 2017-10-04 17:32:58 -04:00
Heng Li 1554149158 r465: apply option -x before other options 2017-10-04 13:52:28 -04:00
Heng Li 19c39e704f r464: fixed a bug in pairing, due to randomization 2017-10-04 13:37:40 -04:00
Heng Li 2581c44a21 r463: optionally disable secondary hits 2017-10-04 13:24:41 -04:00
Heng Li 5babf41a38 r462: SAM primary flag not properly set 2017-10-04 13:11:29 -04:00
Heng Li 2a1e738a94 r461: randomize repetitive hits 2017-10-04 13:05:18 -04:00
Heng Li cf55c84056 r460: added option --no-long-join 2017-10-04 12:08:44 -04:00
Heng Li 841763ec24 Merge branch 'master' into sr 2017-10-04 11:42:44 -04:00
Heng Li 95eb1dec36 r458: fixed wrong chr for inversion aln (#30) 2017-10-04 11:32:06 -04:00
Heng Li 0fd0f2aed1 r457: fixed a bug on parsing -f 2017-09-30 00:00:44 -04:00
Heng Li ee9b2773a8 r456: min chain score should >k-mer length 
or chain_dp() wastes time on unnecessarily sorting chains with one k-mer.
 2017-09-29 22:33:55 -04:00
Heng Li 340483821e r455: set max_occ on command line 2017-09-29 22:18:43 -04:00
Heng Li 04fb2c2ec0 r454: rechain with higher max_occ if no good chain 2017-09-29 19:24:32 -04:00
Heng Li 0d4ecd19ee r453: avoid duplicated strcmp() for ava 2017-09-28 15:52:05 -04:00
Heng Li 0c63325985 r452: fixed - -G not working with -x sr 2017-09-28 14:28:12 -04:00
Heng Li 2a554a92e9 r451: changed rep_len mapq heuristic 2017-09-28 14:23:14 -04:00
Heng Li 935a6e6064 r450: differentiate exact repeats via mapq 2017-09-27 23:51:05 -04:00
Heng Li a13691d00d eval script works with /[12] in SAM 2017-09-27 23:33:59 -04:00
Heng Li 8301222174 r448: fixed a bug when computing PE quality 2017-09-27 21:54:07 -04:00
Heng Li 9541052564 r447: paired-end mapping quality 
not as good as I would hope...
 2017-09-27 15:39:25 -04:00
Heng Li 7e0d70bfd3 r445: pair coordinate adjustment working 
Next: mapq adjustment, which will be tricky...
 2017-09-27 15:38:18 -04:00
Heng Li a349d85280 r444: changed the way orientation is specified 
The old model doesn't work with RF or RR orientation. The new model only works
with paired-end reads. For >2 segments, only FF is supported.
 2017-09-27 12:33:10 -04:00
Heng Li f611edf6f2 r443: don't filter small cm for split seg 2017-09-26 16:17:58 -04:00
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