0fe1a224ab
r309: improved SAM header output
2017-08-25 10:35:58 +08:00
2cde8d257c
r297: bidirectional RNA alignment
2017-08-17 06:02:44 -04:00
b5f5929bf9
r296: expose splicing related options to CLI
2017-08-13 21:37:51 -04:00
43506edbc5
backup: preliminary boundary alignment
2017-08-12 23:10:14 -04:00
d240318741
r287: refined CLI options and manpage
2017-08-12 12:26:04 -04:00
1a7d782131
r273: cdna mapping mode for testing
...
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
...
cs encodes the query, the reference sequence and CIGAR.
2017-07-31 12:06:49 -04:00
19d6ec885e
r224: inversion alignment around Z-drop break
2017-07-29 13:09:10 -04:00
f81f37fef1
r197: allocate index seq names from kalloc
...
to reduce malloc() overhead.
2017-07-24 19:36:05 -04:00
5c4d040b13
r191: warning if CLI index opt diff from prebuilt
...
Also added index testing API (moved from main.c to index.c)
2017-07-19 10:25:11 -04:00
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
b4280d186f
r176: removed seedcov_ratio; changed default opt
...
min_seedcov_ratio is not used
2017-07-12 12:47:46 -04:00
801bc84b01
r169: output more accurate col. 10&11 to PAF
...
In r168, col.10 is smaller than what it should be. This confuses miniasm.
2017-07-11 14:09:51 -04:00
cc554aee43
r159: use two-piece gap penalty
2017-07-08 10:26:00 -04:00
9823317e8f
r158: optionally ignore base quality
2017-07-05 18:23:50 -04:00
53c4bf5e4f
r149: introduced debugging flags on CLI
2017-07-03 11:02:32 -04:00
632b8638d2
r144: adjust primary aln after cigar
2017-07-02 22:43:02 -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
...
otherwise we may get too many poor overlap mappings.
2017-06-30 22:15:45 -04:00
d11049eb32
r120: use max-scoring seg to control output
...
much better now
2017-06-30 14:21:44 -04:00
52b4d8e2c9
r115: set primary tag; still buggy
2017-06-29 23:48:35 -04:00
11167f511b
r112: output z-drop
2017-06-29 22:08:46 -04:00
c8d122bcdb
backup
2017-06-29 11:11:15 -04:00
bcd9b1c621
r93: fixed various small issues
2017-06-28 10:35:21 -04:00
fa80177e58
r89: added minimal number of minimizer counts
2017-06-27 18:43:15 -04:00
640b1a1727
command-line option to control CIGAR output
2017-06-26 11:41:09 -04:00
b1077ff14c
sam output
2017-06-25 22:05:20 -04:00
aa5881e7bb
backup
2017-06-24 22:51:31 -04:00
35b84f88c6
backup
2017-06-23 22:42:15 -04:00
4fea3d778a
backup
2017-06-23 18:57:00 -04:00
6c8368c24c
get the left-extension sequence correctly
2017-06-23 18:25:47 -04:00
990f7b0b71
backup
2017-06-23 15:13:53 -04:00
4ae0b46972
min_ksw_len
2017-06-23 14:38:28 -04:00
9cd313eae1
sequence retrieval working
2017-06-23 14:11:56 -04:00
326d91deb0
backup
2017-06-23 14:06:00 -04:00
44cdd18de0
start to work on alignment
2017-06-23 13:44:45 -04:00
b04e4b9215
r36: bring back primary; don't output all mappings
2017-06-08 15:28:19 -04:00
19e43571c1
r34: removed a bit unused code
2017-06-07 14:35:57 -04:00
8ad5cfde42
output PAF
2017-06-07 14:18:32 -04:00
6d4348db44
dp chaining mostly works, but fails sometimes
...
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
acc7382a30
backup
2017-06-04 16:09:45 -04:00
7b7fabef4d
added idx_stat
2017-04-26 22:52:28 +08:00
de367a340c
compilable again
2017-04-26 19:36:46 +08:00
56723ad580
moved `sum_len` out of the index
...
as it can be inferred.
2017-04-19 11:06:24 -04:00
f5cdd3f72f
is_hpc is a property of the index
2017-04-07 15:42:33 -04:00
b3bc4911ba
index can be compiled; not tested yet
2017-04-07 15:30:30 -04:00
01baa847a1
Homopolymer-compressed k-mer sketch
2017-04-06 15:37:34 -04:00
Heng Li