Heng Li
|
64c1389e1a
|
Merge branch 'master' into splice
|
2017-08-17 23:39:27 +08:00 |
|
Heng Li
|
bbb37d95f2
|
support inserting RG lines
|
2017-08-17 23:34:09 +08:00 |
|
Heng Li
|
2cde8d257c
|
r297: bidirectional RNA alignment
|
2017-08-17 06:02:44 -04:00 |
|
Heng Li
|
c59b0781bc
|
r280: output introns as "N" in the cdna mode
|
2017-08-09 11:45:02 -04:00 |
|
Heng Li
|
12cea727b8
|
r238: bugfix to cs - rev sequence not complemented
|
2017-08-01 10:33:21 -04:00 |
|
Heng Li
|
cd105b47f2
|
r237: fixed a bug in outputting cs:Z
|
2017-07-31 14:49:39 -04:00 |
|
Heng Li
|
35f232c3fa
|
r236: in cs tag, output differences in lowercase
for easy eyeballing
|
2017-07-31 12:17:48 -04:00 |
|
Heng Li
|
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 |
|
Heng Li
|
19d6ec885e
|
r224: inversion alignment around Z-drop break
|
2017-07-29 13:09:10 -04:00 |
|
Heng Li
|
2179e9e24b
|
r221: output SA in the SAM output
|
2017-07-28 23:08:39 -04:00 |
|
Heng Li
|
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 |
|
Heng Li
|
b9b0b6f49c
|
r187: fixed non-terminated sam output (#3)
Only happen to unmapped read, with quality, and in the SAM output
|
2017-07-18 15:20:29 -04:00 |
|
Heng Li
|
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 |
|
Heng Li
|
4ee3202539
|
r164: unmapped read not properly flagged
|
2017-07-08 18:16:18 -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
|
52b4d8e2c9
|
r115: set primary tag; still buggy
|
2017-06-29 23:48:35 -04:00 |
|
Heng Li
|
c4871f380c
|
r114: make SAM output better
|
2017-06-29 23:08:41 -04:00 |
|
Heng Li
|
11167f511b
|
r112: output z-drop
|
2017-06-29 22:08:46 -04:00 |
|
Heng Li
|
4cd456b9ba
|
r108: refactoring, move reg1 routines to hit.c
|
2017-06-29 19:44:11 -04:00 |
|
Heng Li
|
4b8e88a5f4
|
use long options
|
2017-06-26 12:31:36 -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 |