Heng Li
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4c0713ee14
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r235: optionally output tag cs in PAF
cs encodes the query, the reference sequence and CIGAR.
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2017-07-31 12:06:49 -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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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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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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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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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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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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826c8ba892
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r170: added a debugging flag
something wrong with chaining
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2017-07-11 14:47:35 -04:00 |
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Heng Li
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e07daad7ad
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r153: sam primary record not set sometimes
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2017-07-03 13:18:57 -04:00 |
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Heng Li
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53c4bf5e4f
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r149: introduced debugging flags on CLI
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2017-07-03 11:02:32 -04:00 |
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Heng Li
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2e4fd9f1d0
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r148: revamped regs handling after cigar
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2017-07-03 10:44:26 -04:00 |
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Heng Li
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74d306a596
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fixed bug when retaining 2ndary aln; still buggy
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2017-07-02 19:08:30 -04:00 |
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Heng Li
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426c2975f6
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r126: filter by fraction of seed coverage
otherwise we may get too many poor overlap mappings.
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2017-06-30 22:15:45 -04:00 |
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Heng Li
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646a746cdc
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r122: filter contained aln after DP extension
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2017-06-30 15:23:30 -04:00 |
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Heng Li
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1a903486b9
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r118: bugfix - regs unsorted before filtering
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2017-06-30 12:52:28 -04:00 |
|
Heng Li
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11167f511b
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r112: output z-drop
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2017-06-29 22:08:46 -04:00 |
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Heng Li
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4cd456b9ba
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r108: refactoring, move reg1 routines to hit.c
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2017-06-29 19:44:11 -04:00 |
|
Heng Li
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ecedfe5788
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code refactoring for mm_reg1_t
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2017-06-29 19:35:38 -04:00 |
|
Heng Li
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d274e1b743
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backup
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2017-06-29 12:58:52 -04:00 |
|
Heng Li
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c8d122bcdb
|
backup
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2017-06-29 11:11:15 -04:00 |
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Heng Li
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cdc2a1e29f
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r92: fixed a bug for overlapping alignment
On the PBcR example E. coli reads, miniasm gives one circular unitig.
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2017-06-27 22:03:31 -04:00 |
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Heng Li
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fa80177e58
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r89: added minimal number of minimizer counts
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2017-06-27 18:43:15 -04:00 |
|
Heng Li
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b1077ff14c
|
sam output
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2017-06-25 22:05:20 -04:00 |
|
Heng Li
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39083be9ab
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separated formating printing
for SAM in future; and for performance
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2017-06-25 16:13:54 -04:00 |
|
Heng Li
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ef5dd318ca
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implemented chain splitting; NOT tested!!!
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2017-06-24 22:57:43 -04:00 |
|
Heng Li
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aa5881e7bb
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backup
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2017-06-24 22:51:31 -04:00 |
|
Heng Li
|
44cdd18de0
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start to work on alignment
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2017-06-23 13:44:45 -04:00 |
|
Heng Li
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a2958a4836
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minor tweaks
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2017-06-06 15:31:21 -04:00 |
|
Heng Li
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6d4348db44
|
dp chaining mostly works, but fails sometimes
which means there are bugs that need to be fixed
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2017-06-06 14:19:50 -04:00 |
|
Heng Li
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1a9fc04cf0
|
backup
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2017-06-06 10:16:33 -04:00 |