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Author SHA1 Message Date
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
Heng Li 0031158936 Merge branch 'master' into short 2017-09-07 11:41:32 -04:00
Heng Li ef3f7ea2f2 Release minimap2-2.1.1 (r341) 2017-09-06 13:46:51 -04:00
Heng Li 8b9f2aaf04 r339: improved SIMD detection 
old code does not check AVX2
 2017-09-05 13:10:30 -04:00
Heng Li 46e8b6a4f9 r338: portable CPU dispatch, which is the default 
working with gcc, icc, clang and msvc.
 2017-09-03 20:29:24 -04:00
Heng Li 3c997ca016 r337: support CPU dispatch for gcc-4.8+ 
using __builtin_cpu_supports()
 2017-09-03 14:29:49 -04:00
Heng Li f9ccc522cd Merge branch 'master' into short 2017-09-03 11:58:15 -04:00
Heng Li 101b8bb97d r335: report an error if query can't be opened 2017-09-03 11:54:38 -04:00
Heng Li f4a71d447f Merge branch 'master' of github.com:lh3/minimap2 2017-09-03 11:07:32 -04:00
Heng Li 6db9b7579c Better MSVC support 
* get rid of alloca()
* no variable-sized arrays
 2017-09-03 11:05:55 -04:00
Heng Li f50b9a14a7 last commit can't be compiled 2017-09-02 21:07:19 -04:00
Heng Li 33423e1568 get rid of the last var-sized array in ksort 
for MSVC
 2017-09-02 21:05:03 -04:00
Heng Li aeb6b5eeb1 fixed an issue due to the 64-bit assumption 2017-09-02 19:29:52 -04:00
Heng Li 3d3fde8224 replaced remaining alloca() 2017-09-02 18:50:42 -04:00
Heng Li 6f4cbf4f12 ok, %zu is a C99 feature... 2017-09-02 18:48:14 -04:00
Heng Li 2a5d5b6f12 print size_t with %zu instead of %lu 2017-09-02 18:37:48 -04:00
Heng Li 3d48516885 reduced a heap allocation 
which *might* be frequent for short reads
 2017-09-02 18:32:45 -04:00
Heng Li 00416c76d1 for MinGW32 compatibility 
get rid of alloca()
 2017-09-02 18:23:29 -04:00
Heng Li 2b8681ead7 fixed memory leak in example 2017-09-02 17:55:25 -04:00
Heng Li 0a3ebdc916 for better windows compatibility 2017-09-02 17:52:33 -04:00
Heng Li b97620afed moved gettimeofday() to misc.c 2017-09-02 17:40:10 -04:00
Heng Li 743d26eab0 Merge pull request #20 from nanoporetech/msvc14 
ONT source code changes to compile with MSVC 14
 2017-09-02 14:35:02 -07:00
Heng Li 62535ecd7f Merge branch 'dev' 2017-09-01 10:06:21 -07:00
Heng Li 40665d1083 Merge pull request #23 from simonrharris/segfaultfix 
Fixed segfault caused when reading from index file
 2017-09-02 00:46:55 +08:00
Heng Li d4074874ee r316: get rid of a harmless gcc warning 2017-09-01 20:25:27 +08:00
Heng Li eccdb3a1ca r315: added getopt from musl 2017-09-01 20:20:34 +08:00
Heng Li c4080aaf7e Merge branch 'master' into short 2017-08-28 07:02:22 +08:00
Heng Li 2641613686 various minor improvements 2017-08-25 17:56:16 +08:00
Heng Li 5f96d851a8 added spliced alignment example 2017-08-25 14:11:54 +08:00
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 079ec0d283 r271: added "short" preset; for testing only 2017-08-07 15:30:05 -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