Heng Li
|
71c988f6ab
|
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 |
|
Heng Li
|
71e2a97a4c
|
r180: changed -x asm5 settings
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2017-07-18 00:00:36 -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 |
|
Heng Li
|
52caf79395
|
r175: halved max-chain-skip in the ava mode
|
2017-07-12 10:42:19 -04:00 |
|
Heng Li
|
eeeb2ffb68
|
r174: make max-chain-skip work
The max-chain-skip heuristics did not work due to a bug. Without this
heuristics, chaining is too slow for long-read overlap.
|
2017-07-12 10:08:06 -04:00 |
|
Heng Li
|
33451aba45
|
r173: changed the debugging output format
|
2017-07-11 15:23:28 -04:00 |
|
Heng Li
|
826c8ba892
|
r170: added a debugging flag
something wrong with chaining
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2017-07-11 14:47:35 -04:00 |
|
Heng Li
|
1ac48556ae
|
r167: long join threshold depends on gap
also caught a bug for reverse strand join
|
2017-07-09 10:38:51 -04:00 |
|
Heng Li
|
42846ce65d
|
r163: reduced long join score requirement
because the chaining score is generally smaller with the last few commits.
|
2017-07-08 15:51:52 -04:00 |
|
Heng Li
|
38b2830e18
|
r161: filter bad seeds; changed default -g/-r
|
2017-07-08 13:31:27 -04:00 |
|
Heng Li
|
cc554aee43
|
r159: use two-piece gap penalty
|
2017-07-08 10:26:00 -04:00 |
|
Heng Li
|
9823317e8f
|
r158: optionally ignore base quality
|
2017-07-05 18:23:50 -04:00 |
|
Heng Li
|
e07daad7ad
|
r153: sam primary record not set sometimes
|
2017-07-03 13:18:57 -04:00 |
|
Heng Li
|
b625247300
|
r150: mm_sync_regs() doesn't work with negative id
|
2017-07-03 11:36:34 -04:00 |
|
Heng Li
|
53c4bf5e4f
|
r149: introduced debugging flags on CLI
|
2017-07-03 11:02:32 -04:00 |
|
Heng Li
|
2e4fd9f1d0
|
r148: revamped regs handling after cigar
|
2017-07-03 10:44:26 -04:00 |
|
Heng Li
|
51cfb60520
|
r145: changed default -p from 2 to 0.8
For long reads, secondary alignments can be very information.
|
2017-07-02 22:51:45 -04:00 |
|
Heng Li
|
74d306a596
|
fixed bug when retaining 2ndary aln; still buggy
|
2017-07-02 19:08:30 -04:00 |
|
Heng Li
|
41efd03d7a
|
r129: fixed memory leak caused by qualities
|
2017-06-30 23:48:00 -04:00 |
|
Heng Li
|
426c2975f6
|
r126: filter by fraction of seed coverage
otherwise we may get too many poor overlap mappings.
|
2017-06-30 22:15:45 -04:00 |
|
Heng Li
|
646a746cdc
|
r122: filter contained aln after DP extension
|
2017-06-30 15:23:30 -04:00 |
|
Heng Li
|
fce87ce7bd
|
r121: output QUAL and unmapped to SAM
|
2017-06-30 14:40:54 -04:00 |
|
Heng Li
|
d11049eb32
|
r120: use max-scoring seg to control output
much better now
|
2017-06-30 14:21:44 -04:00 |
|
Heng Li
|
1a903486b9
|
r118: bugfix - regs unsorted before filtering
|
2017-06-30 12:52:28 -04:00 |
|
Heng Li
|
03267e8fa7
|
r113: fixed a sam header bug
|
2017-06-29 22:43:06 -04:00 |
|
Heng Li
|
3825feeeac
|
r111: changed the default z-drop to 200
|
2017-06-29 21:37:56 -04:00 |
|
Heng Li
|
08cbb09fcc
|
r109: changed the default scoring
|
2017-06-29 20:21:57 -04:00 |
|
Heng Li
|
4cd456b9ba
|
r108: refactoring, move reg1 routines to hit.c
|
2017-06-29 19:44:11 -04:00 |
|
Heng Li
|
ecedfe5788
|
code refactoring for mm_reg1_t
|
2017-06-29 19:35:38 -04:00 |
|
Heng Li
|
cc67f1b781
|
compute mapq; not working for z-split yet
|
2017-06-29 17:52:48 -04:00 |
|
Heng Li
|
b9075d39a8
|
r104: long gap patching
|
2017-06-29 14:54:54 -04:00 |
|
Heng Li
|
17944a75c2
|
merge into map.c
|
2017-06-29 14:20:14 -04:00 |
|
Heng Li
|
c8d122bcdb
|
backup
|
2017-06-29 11:11:15 -04:00 |
|
Heng Li
|
9fbf7e41e1
|
r99: report progress
|
2017-06-28 23:56:33 -04:00 |
|
Heng Li
|
b696d5fe5e
|
disable kalloc in the debugging mode
|
2017-06-28 10:50:27 -04:00 |
|
Heng Li
|
bcd9b1c621
|
r93: fixed various small issues
|
2017-06-28 10:35:21 -04:00 |
|
Heng Li
|
cdc2a1e29f
|
r92: fixed a bug for overlapping alignment
On the PBcR example E. coli reads, miniasm gives one circular unitig.
|
2017-06-27 22:03:31 -04:00 |
|
Heng Li
|
533150d49d
|
r90: revert default band width to 1000
10000 is excessively tolerant with bad hits.
|
2017-06-27 20:29:39 -04:00 |
|
Heng Li
|
fa80177e58
|
r89: added minimal number of minimizer counts
|
2017-06-27 18:43:15 -04:00 |
|
Heng Li
|
99c57b86c5
|
r79: drop bad hits
|
2017-06-26 15:28:04 -04:00 |
|
Heng Li
|
5b614ae828
|
r78: fixed a split bug
|
2017-06-26 14:45:23 -04:00 |
|
Heng Li
|
de54c9dac2
|
r77: fixed an index loading bug (offset not set)
|
2017-06-26 13:56:25 -04:00 |
|
Heng Li
|
640b1a1727
|
command-line option to control CIGAR output
|
2017-06-26 11:41:09 -04:00 |
|
Heng Li
|
b1077ff14c
|
sam output
|
2017-06-25 22:05:20 -04:00 |
|
Heng Li
|
39083be9ab
|
separated formating printing
for SAM in future; and for performance
|
2017-06-25 16:13:54 -04:00 |
|
Heng Li
|
f20d550a59
|
fixed the NM bug
due to reversed CIGAR
|
2017-06-25 11:24:39 -04:00 |
|
Heng Li
|
ef5dd318ca
|
implemented chain splitting; NOT tested!!!
|
2017-06-24 22:57:43 -04:00 |
|
Heng Li
|
aa5881e7bb
|
backup
|
2017-06-24 22:51:31 -04:00 |
|
Heng Li
|
2d8fda9586
|
an alternative strategy to fix for HPC
it makes the result better, but still not quite right.
|
2017-06-24 09:26:24 -04:00 |
|
Heng Li
|
0c274280ae
|
output the original score
|
2017-06-23 22:56:50 -04:00 |