da7109fd29
r985: optionally report cs/cg on the query strand
...
PAF only; not well tested
2020-04-21 12:37:35 -04:00
7996f04008
r972: fixed negative de:f caused by ambiguous base
2020-01-21 09:14:37 -05:00
3c0d05d272
r962: abort given wrong RG line; resolves #541
2020-01-06 21:53:21 -05:00
371bc9513a
SAM TLEN should be 0 when either read is unmapped
...
this_rid/this_pos will be copied from r_prev(=r_next)'s values when this
read is unmapped (i.e., r is NULL). In this case, we can write RNEXT as
'=' but should not calculate TLEN from these placeholder values.
Similarly when the mate is unmapped (i.e., r_next is NULL).
Fixes #365 .
2019-04-05 09:36:46 -04:00
55e39c2d30
r921: output unmapped reads in full PAF
2019-02-27 15:03:19 -05:00
1739a260fb
r913: output tag "rl", length of unseedable regs
2019-02-05 14:19:17 -05:00
597212b9f3
r908: added an assertion to detect a potential bug
...
as in #311
2019-01-23 11:18:50 -05:00
48e230f40d
r906: de tag is wrongly calculated given "N"
...
Resolves #309
2019-01-11 19:39:09 -05:00
2c52364527
r892: avoid de:f:0.0000
2018-11-24 21:54:28 -05:00
128476efc9
r891: compute gap-compressed divergence
2018-11-24 21:50:49 -05:00
a8ee48c2ce
r873: comforming to C99/C11; resolves #261
2018-11-05 08:25:07 -05:00
9ed56b4a25
r860: MD/cs not working with --eqx
2018-10-26 23:23:53 -04:00
7d80d6de4a
r832: fixed outdated -L. Resolved #231 and #233
2018-09-14 22:21:33 -04:00
3a119d606f
r828: --MD to support spliced alignment
2018-08-22 10:47:45 -04:00
ff9917a1c4
r819: mappy to support cs/MD
2018-07-24 23:29:55 -04:00
a609a07f8c
optionally output unmapped query in PAF
2018-07-07 10:26:08 -05:00
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
154d2caf5b
r784: support the =/X CIGAR operators ( #156 )
2018-05-30 16:11:22 -04:00
08bd2123b6
r752: option to copy comments to output ( #136 )
2018-03-23 10:04:33 -04:00
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
...
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
...
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
Heng Li
John Marshall
mvdbeek
Shane McCarthy