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 |
|
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 |
|
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 |
|
Heng Li
|
5c4d040b13
|
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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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 |
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Heng Li
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b4280d186f
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r176: removed seedcov_ratio; changed default opt
min_seedcov_ratio is not used
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2017-07-12 12:47:46 -04:00 |
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Heng Li
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801bc84b01
|
r169: output more accurate col. 10&11 to PAF
In r168, col.10 is smaller than what it should be. This confuses miniasm.
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2017-07-11 14:09:51 -04:00 |
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Heng Li
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cc554aee43
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r159: use two-piece gap penalty
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2017-07-08 10:26:00 -04:00 |
|
Heng Li
|
9823317e8f
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r158: optionally ignore base quality
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2017-07-05 18:23:50 -04:00 |
|
Heng Li
|
53c4bf5e4f
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r149: introduced debugging flags on CLI
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2017-07-03 11:02:32 -04:00 |
|
Heng Li
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632b8638d2
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r144: adjust primary aln after cigar
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2017-07-02 22:43:02 -04:00 |
|
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 |
|
Heng Li
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d11049eb32
|
r120: use max-scoring seg to control output
much better now
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2017-06-30 14:21:44 -04:00 |
|
Heng Li
|
52b4d8e2c9
|
r115: set primary tag; still buggy
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2017-06-29 23:48:35 -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 |
|
Heng Li
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c8d122bcdb
|
backup
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2017-06-29 11:11:15 -04:00 |
|
Heng Li
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bcd9b1c621
|
r93: fixed various small issues
|
2017-06-28 10:35:21 -04:00 |
|
Heng Li
|
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
|
640b1a1727
|
command-line option to control CIGAR output
|
2017-06-26 11:41:09 -04:00 |
|
Heng Li
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b1077ff14c
|
sam output
|
2017-06-25 22:05:20 -04:00 |
|
Heng Li
|
aa5881e7bb
|
backup
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2017-06-24 22:51:31 -04:00 |
|
Heng Li
|
35b84f88c6
|
backup
|
2017-06-23 22:42:15 -04:00 |
|
Heng Li
|
4fea3d778a
|
backup
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2017-06-23 18:57:00 -04:00 |
|
Heng Li
|
6c8368c24c
|
get the left-extension sequence correctly
|
2017-06-23 18:25:47 -04:00 |
|
Heng Li
|
990f7b0b71
|
backup
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2017-06-23 15:13:53 -04:00 |
|
Heng Li
|
4ae0b46972
|
min_ksw_len
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2017-06-23 14:38:28 -04:00 |
|
Heng Li
|
9cd313eae1
|
sequence retrieval working
|
2017-06-23 14:11:56 -04:00 |
|
Heng Li
|
326d91deb0
|
backup
|
2017-06-23 14:06:00 -04:00 |
|
Heng Li
|
44cdd18de0
|
start to work on alignment
|
2017-06-23 13:44:45 -04:00 |
|
Heng Li
|
b04e4b9215
|
r36: bring back primary; don't output all mappings
|
2017-06-08 15:28:19 -04:00 |
|
Heng Li
|
19e43571c1
|
r34: removed a bit unused code
|
2017-06-07 14:35:57 -04:00 |
|
Heng Li
|
8ad5cfde42
|
output PAF
|
2017-06-07 14:18:32 -04:00 |
|
Heng Li
|
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 |
|
Heng Li
|
1a9fc04cf0
|
backup
|
2017-06-06 10:16:33 -04:00 |
|
Heng Li
|
acc7382a30
|
backup
|
2017-06-04 16:09:45 -04:00 |
|
Heng Li
|
7b7fabef4d
|
added idx_stat
|
2017-04-26 22:52:28 +08:00 |
|
Heng Li
|
de367a340c
|
compilable again
|
2017-04-26 19:36:46 +08:00 |
|
Heng Li
|
56723ad580
|
moved `sum_len` out of the index
as it can be inferred.
|
2017-04-19 11:06:24 -04:00 |
|
Heng Li
|
f5cdd3f72f
|
is_hpc is a property of the index
|
2017-04-07 15:42:33 -04:00 |
|
Heng Li
|
b3bc4911ba
|
index can be compiled; not tested yet
|
2017-04-07 15:30:30 -04:00 |
|
Heng Li
|
01baa847a1
|
Homopolymer-compressed k-mer sketch
|
2017-04-06 15:37:34 -04:00 |