8766d286df
r751: optionally output MD ( #118 )
2018-03-22 14:15:33 -04:00
623b5d9d48
r750: check puts() return ( #132 & #103 )
2018-03-22 11:31:58 -04:00
0e42628ef6
r611: document --idx-no-seq; better inv aln
2017-12-08 13:16:18 -05:00
704ff9f4c6
r607: estimate sequence divergence
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Currently using the simplest method. There may be a more accurate estimate.
2017-12-06 16:14:39 -05:00
99a2709913
r567: minor change to #56
2017-11-09 19:17:45 -05:00
1cb0bf4bef
Implement -Y for soft clipping of supp. alignments
...
I tried to base this on bwa-mem and it seems to work for sam alignments.
2017-11-09 19:22:36 +01:00
b24d68ae9f
r557: fixed another mapq underestimate
...
When a chain is split during base-level alignment, its chaining score is
reduced. However, the chaining score of its suboptimal chain remains the same.
This leads to underestimated mapping quality.
2017-11-07 23:20:49 -05:00
a3f0aa1d5b
r550: fixed -L issues with secondary and supp aln
2017-11-04 12:13:38 -04:00
4683da2455
r520: added option -L to write long cigar to CG
2017-10-17 17:32:44 -04:00
adf6cd7f52
r513: merged pre- and post-cigar blen and mlen
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This saves a bit memory and is cleaner.
2017-10-16 10:55:18 -04:00
e6f525edaf
r512: option to filter poorly aligned reads
2017-10-16 10:38:22 -04:00
dea3b60918
r510: fixed an off-by-1 bug for unmapped mate
2017-10-12 17:31:13 -04:00
5498565157
fix sam output for some unmapped queries
2017-10-11 08:46:24 +01:00
ca632f907b
r498: fixed a bug when merging like "4I5I"
2017-10-10 21:22:37 -04:00
e0baf1ad54
r479: a bit code cleanup
2017-10-05 16:15:14 -04:00
f4a5d3a692
r474: replaced -S and --cs-no-equal with --cs
2017-10-05 15:03:03 -04:00
1a90bc8603
r472: fixed a bug when printing MAPQ/CIGAR
2017-10-05 12:46:11 -04:00
abf2a90363
r471: all SAM features implemented; more tests!
2017-10-05 12:37:30 -04:00
5ab99eb26e
more accurate SAM flag
2017-10-05 10:59:38 -04:00
7cc4f6f965
r469: first step towards PE SAM
2017-10-05 10:38:09 -04:00
16e6e589a8
r468: replaced ^ with ~ in cs
2017-10-04 22:17:12 -04:00
9aba11769c
r467: added : (equal length) and ^ (intron) ops
2017-10-04 21:55:37 -04:00
7d50e646dd
r466: detect multi-part index more smartly
...
though it might not work in an extremely rare case: the end of a sequence ends
at X*16384 and it is the last sequence in a batch. This can be resolved by
never letting the kstream_t buffer empty.
2017-10-04 17:32:58 -04:00
3bb66e1ed3
multi-seg working on toy examples
2017-09-25 13:42:04 -04:00
0fe1a224ab
r309: improved SAM header output
2017-08-25 10:35:58 +08:00
993a2bb521
r301: separate introns from deletions
...
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
c59b0781bc
r280: output introns as "N" in the cdna mode
2017-08-09 11:45:02 -04:00
12cea727b8
r238: bugfix to cs - rev sequence not complemented
2017-08-01 10:33:21 -04:00
cd105b47f2
r237: fixed a bug in outputting cs:Z
2017-07-31 14:49:39 -04:00
35f232c3fa
r236: in cs tag, output differences in lowercase
...
for easy eyeballing
2017-07-31 12:17:48 -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
2179e9e24b
r221: output SA in the SAM output
2017-07-28 23:08:39 -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
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
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
4ee3202539
r164: unmapped read not properly flagged
2017-07-08 18:16:18 -04:00
fce87ce7bd
r121: output QUAL and unmapped to SAM
2017-06-30 14:40:54 -04:00
d11049eb32
r120: use max-scoring seg to control output
...
much better now
2017-06-30 14:21:44 -04:00
1a903486b9
r118: bugfix - regs unsorted before filtering
2017-06-30 12:52:28 -04:00
52b4d8e2c9
r115: set primary tag; still buggy
2017-06-29 23:48:35 -04:00
c4871f380c
r114: make SAM output better
2017-06-29 23:08:41 -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
4b8e88a5f4
use long options
2017-06-26 12:31:36 -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
Heng Li
mvdbeek
Shane McCarthy