Heng Li
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46de0fbdad
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Merge pull request #8 from rikuu/master
fix self-comparison in index parameter override check
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2017-07-30 15:10:29 -04:00 |
Riku Walve
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9e09c1ae72
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fix self-comparison in index parameter override check
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2017-07-30 21:46:25 +03:00 |
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Heng Li
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d8d4d29b68
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Release minimap2-2.0rc1-r232
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2017-07-30 14:32:40 -04:00 |
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Heng Li
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e51dfd0330
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added NEWS
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2017-07-30 14:20:03 -04:00 |
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Heng Li
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1f78e1ee53
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r230: code formatting changes only
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2017-07-30 12:31:40 -04:00 |
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Heng Li
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5934d68772
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r229: a new way to prevent out-of-band backtrack
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2017-07-29 23:52:30 -04:00 |
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Heng Li
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fa99d28d34
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r228: reduced unnecessary INV alignment
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2017-07-29 20:21:53 -04:00 |
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Heng Li
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d08b7a0c51
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r227: use local alignment for INV alignment
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2017-07-29 17:40:53 -04:00 |
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Heng Li
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da3db3c095
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r226: only try inv alignment for primary
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2017-07-29 14:09:35 -04:00 |
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Heng Li
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783ead6f47
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r225: removed a debugging line
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2017-07-29 13:21:38 -04:00 |
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Heng Li
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19d6ec885e
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r224: inversion alignment around Z-drop break
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2017-07-29 13:09:10 -04:00 |
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Heng Li
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120bebc290
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ake
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2017-07-29 11:01:49 -04:00 |
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Heng Li
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5e3eecd6d4
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r222: no effective changes
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2017-07-29 10:31:46 -04:00 |
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Heng Li
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2179e9e24b
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r221: output SA in the SAM output
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2017-07-28 23:08:39 -04:00 |
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Heng Li
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84922cfe41
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clarify that wrong seeding mainly occurs in LCRs
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2017-07-28 14:33:15 -04:00 |
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Heng Li
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ebbe9c1eb8
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r219: fixed a bug caused by skipping tandem seeds
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2017-07-28 14:06:56 -04:00 |
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Heng Li
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c672690564
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r218: increase the frequency of SW slightly
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2017-07-28 13:30:42 -04:00 |
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Heng Li
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f4fee60188
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r217: ignore tandem seeds during alignment
This helps a tiny bit.
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2017-07-28 12:26:56 -04:00 |
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Heng Li
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254280b8af
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r216: a bit cleanup; identical output to r215
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2017-07-28 11:54:18 -04:00 |
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Heng Li
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fc965805f7
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r215: bring back a log gap component
Otherwise chaining may more often break a long gap into several gaps.
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2017-07-28 00:17:19 -04:00 |
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Heng Li
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667b32a516
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added algorithm overview
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2017-07-27 18:50:39 -04:00 |
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Heng Li
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2c79580649
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r213: more careful solution to wrong seeds
a little better, but not good enough!
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2017-07-27 13:19:11 -04:00 |
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Heng Li
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b927838495
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r212: better heuristic to fix wrong seeding
but not good enough. Will explore more.
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2017-07-27 11:24:51 -04:00 |
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Heng Li
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371e20cc7c
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r211: a better heurstic to reduce false seeds
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2017-07-26 23:56:38 -04:00 |
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Heng Li
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8b08a2ec41
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added first-only and all-primary modes to eval
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2017-07-26 19:32:26 -04:00 |
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Heng Li
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9f728dd96a
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tunable overlap ratio
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2017-07-26 18:30:29 -04:00 |
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Heng Li
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323293fbda
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changed the way mapq is counted
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2017-07-26 14:20:31 -04:00 |
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Heng Li
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bd33bed455
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make output better
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2017-07-26 12:03:42 -04:00 |
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Heng Li
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a01d758af6
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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.
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2017-07-26 11:50:04 -04:00 |
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Heng Li
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e9dc1ce2b6
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r205: when computing mapq, consider min_chain_sc
Not doing this was a mistake.
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2017-07-26 11:34:14 -04:00 |
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Heng Li
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a8ad53ee81
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evaluating read mapping for pbsim2fa reads
More functionality to be added later
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2017-07-26 11:17:34 -04:00 |
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Heng Li
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00c6db5073
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r203: check more subopt aln if score small
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2017-07-25 20:02:44 -04:00 |
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Heng Li
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f2ef48878a
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r202: trim bad chain ends before extension
This fixes a few more FP long INDELs towards the end of alignments.
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2017-07-25 19:53:19 -04:00 |
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Heng Li
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21ca564112
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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.
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2017-07-25 18:26:51 -04:00 |
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Heng Li
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215e92ed7b
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r200: reduce long gaps in chaining
Every seed can initiate a chain.
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2017-07-25 17:32:54 -04:00 |
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Heng Li
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b530ade333
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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.
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2017-07-25 15:35:10 -04:00 |
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Heng Li
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4bd7ebc39c
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convert pbsim .maf to fasta
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2017-07-25 13:54:58 -04:00 |
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Heng Li
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f81f37fef1
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r197: allocate index seq names from kalloc
to reduce malloc() overhead.
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2017-07-24 19:36:05 -04:00 |
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Heng Li
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5c4d040b13
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r191: warning if CLI index opt diff from prebuilt
Also added index testing API (moved from main.c to index.c)
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2017-07-19 10:25:11 -04:00 |
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Heng Li
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4aff301ef4
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r190: default -k to 15; added -x map-ont
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2017-07-19 10:11:14 -04:00 |
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Heng Li
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470021fd27
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r189: sync with ksw2 (no effective changes)
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2017-07-19 09:28:25 -04:00 |
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Heng Li
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71c988f6ab
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r188: renamed bseq* to mm_bseq*
to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
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2017-07-19 09:26:46 -04:00 |
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Heng Li
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b9b0b6f49c
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r187: fixed non-terminated sam output (#3)
Only happen to unmapped read, with quality, and in the SAM output
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2017-07-18 15:20:29 -04:00 |
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Heng Li
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947cf162be
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update dependency; delete minimap2-lite on clean
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2017-07-18 14:48:46 -04:00 |
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Heng Li
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293a7049f3
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migrated minimap/example.c here.
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2017-07-18 14:43:43 -04:00 |
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Heng Li
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a1addb2949
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use -msse4 by default, not -march
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2017-07-18 13:56:51 -04:00 |
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Heng Li
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b4edb0cf55
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fixed URL
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2017-07-18 13:26:51 -04:00 |
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Heng Li
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9a935dcef5
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Fixed grammar errors
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2017-07-18 11:37:58 -04:00 |
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Heng Li
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495a78e40a
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Get documentation ready for release
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2017-07-18 11:04:09 -04:00 |
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Heng Li
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71e2a97a4c
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r180: changed -x asm5 settings
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2017-07-18 00:00:36 -04:00 |