993a2bb521
r301: separate introns from deletions
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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
64c1389e1a
Merge branch 'master' into splice
2017-08-17 23:39:27 +08:00
bbb37d95f2
support inserting RG lines
2017-08-17 23:34:09 +08:00
2cde8d257c
r297: bidirectional RNA alignment
2017-08-17 06:02:44 -04:00
0f4c823b0c
r286: ignore introns when computing max seg score
2017-08-12 10:58:16 -04:00
c59b0781bc
r280: output introns as "N" in the cdna mode
2017-08-09 11:45:02 -04:00
1a7d782131
r273: cdna mapping mode for testing
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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
4c0713ee14
r235: optionally output tag cs in PAF
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cs encodes the query, the reference sequence and CIGAR.
2017-07-31 12:06:49 -04:00
5934d68772
r229: a new way to prevent out-of-band backtrack
2017-07-29 23:52:30 -04:00
2179e9e24b
r221: output SA in the SAM output
2017-07-28 23:08:39 -04:00
254280b8af
r216: a bit cleanup; identical output to r215
2017-07-28 11:54:18 -04:00
e9dc1ce2b6
r205: when computing mapq, consider min_chain_sc
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Not doing this was a mistake.
2017-07-26 11:34:14 -04:00
00c6db5073
r203: check more subopt aln if score small
2017-07-25 20:02:44 -04:00
71c988f6ab
r188: renamed bseq* to mm_bseq*
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to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
2017-07-19 09:26:46 -04:00
826c8ba892
r170: added a debugging flag
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something wrong with chaining
2017-07-11 14:47:35 -04:00
e07daad7ad
r153: sam primary record not set sometimes
2017-07-03 13:18:57 -04:00
53c4bf5e4f
r149: introduced debugging flags on CLI
2017-07-03 11:02:32 -04:00
2e4fd9f1d0
r148: revamped regs handling after cigar
2017-07-03 10:44:26 -04:00
74d306a596
fixed bug when retaining 2ndary aln; still buggy
2017-07-02 19:08:30 -04:00
426c2975f6
r126: filter by fraction of seed coverage
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otherwise we may get too many poor overlap mappings.
2017-06-30 22:15:45 -04:00
646a746cdc
r122: filter contained aln after DP extension
2017-06-30 15:23:30 -04:00
1a903486b9
r118: bugfix - regs unsorted before filtering
2017-06-30 12:52:28 -04:00
11167f511b
r112: output z-drop
2017-06-29 22:08:46 -04:00
4cd456b9ba
r108: refactoring, move reg1 routines to hit.c
2017-06-29 19:44:11 -04:00
ecedfe5788
code refactoring for mm_reg1_t
2017-06-29 19:35:38 -04:00
d274e1b743
backup
2017-06-29 12:58:52 -04:00
c8d122bcdb
backup
2017-06-29 11:11:15 -04:00
cdc2a1e29f
r92: fixed a bug for overlapping alignment
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On the PBcR example E. coli reads, miniasm gives one circular unitig.
2017-06-27 22:03:31 -04:00
fa80177e58
r89: added minimal number of minimizer counts
2017-06-27 18:43:15 -04:00
b1077ff14c
sam output
2017-06-25 22:05:20 -04:00
39083be9ab
separated formating printing
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for SAM in future; and for performance
2017-06-25 16:13:54 -04:00
ef5dd318ca
implemented chain splitting; NOT tested!!!
2017-06-24 22:57:43 -04:00
aa5881e7bb
backup
2017-06-24 22:51:31 -04:00
44cdd18de0
start to work on alignment
2017-06-23 13:44:45 -04:00
a2958a4836
minor tweaks
2017-06-06 15:31:21 -04:00
6d4348db44
dp chaining mostly works, but fails sometimes
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which means there are bugs that need to be fixed
2017-06-06 14:19:50 -04:00
1a9fc04cf0
backup
2017-06-06 10:16:33 -04:00
Heng Li