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224 Commits 9 Branches 35 Tags
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Author SHA1 Message Date
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
Heng Li
9f728dd96a tunable overlap ratio 2017-07-26 18:30:29 -04:00
Heng Li
323293fbda changed the way mapq is counted 2017-07-26 14:20:31 -04:00
Heng Li
bd33bed455 make output better 2017-07-26 12:03:42 -04:00
Heng Li
a01d758af6 r206: mapq penalize short chains further 
The old code penalized at the log() scale. Now added a linear-scaled factor. If
the chain consists of few minimizers, its quality is really not good.
 2017-07-26 11:50:04 -04:00
Heng Li
e9dc1ce2b6 r205: when computing mapq, consider min_chain_sc 
Not doing this was a mistake.
 2017-07-26 11:34:14 -04:00
Heng Li
a8ad53ee81 evaluating read mapping for pbsim2fa reads 
More functionality to be added later
 2017-07-26 11:17:34 -04:00
Heng Li
00c6db5073 r203: check more subopt aln if score small 2017-07-25 20:02:44 -04:00
Heng Li
f2ef48878a r202: trim bad chain ends before extension 
This fixes a few more FP long INDELs towards the end of alignments.
 2017-07-25 19:53:19 -04:00
Heng Li
21ca564112 r201: fixed a minor chaining issue 
Chaining looked at the end of a chain, but the end may not be the best. We now
go back to find the max.
 2017-07-25 18:26:51 -04:00
Heng Li
215e92ed7b r200: reduce long gaps in chaining 
Every seed can initiate a chain.
 2017-07-25 17:32:54 -04:00
Heng Li
b530ade333 r199: changed to linear gap cost for chaining 
The old cost doesn't penalize long gaps enough. Will also drop seeds close to
the edge in the next commit.
 2017-07-25 15:35:10 -04:00
Heng Li
4bd7ebc39c convert pbsim .maf to fasta 2017-07-25 13:54:58 -04:00
Heng Li
f81f37fef1 r197: allocate index seq names from kalloc 
to reduce malloc() overhead.
 2017-07-24 19:36:05 -04:00
Heng Li
5c4d040b13 r191: warning if CLI index opt diff from prebuilt 
Also added index testing API (moved from main.c to index.c)
r191 		2017-07-19 10:25:11 -04:00
Heng Li
4aff301ef4 r190: default -k to 15; added -x map-ont 2017-07-19 10:11:14 -04:00
Heng Li
470021fd27 r189: sync with ksw2 (no effective changes) 2017-07-19 09:28:25 -04:00
Heng Li
71c988f6ab r188: renamed bseq* to mm_bseq* 
to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
 2017-07-19 09:26:46 -04:00
Heng Li
b9b0b6f49c r187: fixed non-terminated sam output (#3) 
Only happen to unmapped read, with quality, and in the SAM output
 2017-07-18 15:20:29 -04:00
Heng Li
947cf162be update dependency; delete minimap2-lite on clean 2017-07-18 14:48:46 -04:00
Heng Li
293a7049f3 migrated minimap/example.c here. 2017-07-18 14:43:43 -04:00
Heng Li
a1addb2949 use -msse4 by default, not -march 2017-07-18 13:56:51 -04:00
Heng Li
b4edb0cf55 fixed URL 2017-07-18 13:26:51 -04:00
Heng Li
9a935dcef5 Fixed grammar errors 2017-07-18 11:37:58 -04:00
Heng Li
495a78e40a Get documentation ready for release 2017-07-18 11:04:09 -04:00
Heng Li
71e2a97a4c r180: changed -x asm5 settings 2017-07-18 00:00:36 -04:00
Heng Li
941059292e r179: changed the preset for assembly alignment 2017-07-17 22:41:46 -04:00
Heng Li
38aa66fa30 r178: fixed integer overflow in mapq calculation 2017-07-16 21:45:39 -04:00
Heng Li
f42790398d fixed a band boundary bug in ksw2 2017-07-16 17:52:57 -04:00
Heng Li
b4280d186f r176: removed seedcov_ratio; changed default opt 
min_seedcov_ratio is not used
 2017-07-12 12:47:46 -04:00