56acf6ee28
completed README rewrite
2017-10-06 14:26:02 -04:00
4f6244bd4a
revamped README; not finished yet
2017-10-06 13:02:25 -04:00
c6384ed2c8
r482: increased short-read bandwidth to 100
...
This has very minor effect on speed.
2017-10-06 10:20:32 -04:00
2833a9c255
150bp mason2 simulation
2017-10-06 09:46:59 -04:00
de2fcc1bf3
updated the mappy
2017-10-05 17:10:07 -04:00
e0baf1ad54
r479: a bit code cleanup
2017-10-05 16:15:14 -04:00
f266092699
r478: simplied useless code, a tiny bit
2017-10-05 15:56:00 -04:00
9c5767f9ed
r477: renamed multi_seg to frag_mode
2017-10-05 15:48:17 -04:00
ae2adf04d4
r476: multi-file fragment mode working
2017-10-05 15:39:26 -04:00
b839758335
r475: added --cs=none; updated manpage
2017-10-05 15:27:37 -04:00
f4a5d3a692
r474: replaced -S and --cs-no-equal with --cs
2017-10-05 15:03:03 -04:00
3ff6eda3a4
r473: don't count introns into blen
2017-10-05 14:37:21 -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
1554149158
r465: apply option -x before other options
2017-10-04 13:52:28 -04:00
19c39e704f
r464: fixed a bug in pairing, due to randomization
2017-10-04 13:37:40 -04:00
2581c44a21
r463: optionally disable secondary hits
2017-10-04 13:24:41 -04:00
5babf41a38
r462: SAM primary flag not properly set
2017-10-04 13:11:29 -04:00
2a1e738a94
r461: randomize repetitive hits
2017-10-04 13:05:18 -04:00
cf55c84056
r460: added option --no-long-join
2017-10-04 12:08:44 -04:00
841763ec24
Merge branch 'master' into sr
2017-10-04 11:42:44 -04:00
95eb1dec36
r458: fixed wrong chr for inversion aln ( #30 )
2017-10-04 11:32:06 -04:00
0fd0f2aed1
r457: fixed a bug on parsing -f
2017-09-30 00:00:44 -04:00
ee9b2773a8
r456: min chain score should >k-mer length
...
or chain_dp() wastes time on unnecessarily sorting chains with one k-mer.
2017-09-29 22:33:55 -04:00
340483821e
r455: set max_occ on command line
2017-09-29 22:18:43 -04:00
04fb2c2ec0
r454: rechain with higher max_occ if no good chain
2017-09-29 19:24:32 -04:00
0d4ecd19ee
r453: avoid duplicated strcmp() for ava
2017-09-28 15:52:05 -04:00
0c63325985
r452: fixed - -G not working with -x sr
2017-09-28 14:28:12 -04:00
2a554a92e9
r451: changed rep_len mapq heuristic
2017-09-28 14:23:14 -04:00
935a6e6064
r450: differentiate exact repeats via mapq
2017-09-27 23:51:05 -04:00
a13691d00d
eval script works with /[12] in SAM
2017-09-27 23:33:59 -04:00
8301222174
r448: fixed a bug when computing PE quality
2017-09-27 21:54:07 -04:00
9541052564
r447: paired-end mapping quality
...
not as good as I would hope...
2017-09-27 15:39:25 -04:00
7e0d70bfd3
r445: pair coordinate adjustment working
...
Next: mapq adjustment, which will be tricky...
2017-09-27 15:38:18 -04:00
a349d85280
r444: changed the way orientation is specified
...
The old model doesn't work with RF or RR orientation. The new model only works
with paired-end reads. For >2 segments, only FF is supported.
2017-09-27 12:33:10 -04:00
f611edf6f2
r443: don't filter small cm for split seg
2017-09-26 16:17:58 -04:00
1b1dd0cd57
r442: default max_gap to 200 in the sr mode
2017-09-26 13:31:01 -04:00
92ec8bd859
added the /1 or /2 suffix
2017-09-26 12:04:35 -04:00
55d1e4f638
r440: better chain filtering for PE reads
2017-09-26 11:03:36 -04:00
64c0ad6b35
r439: use splice-like chain gap cost between segs
...
This improves accuracy
2017-09-25 16:04:38 -04:00
9538c985aa
r438: fixed a rare case that leads to missing hits
...
It is a bug in chaining.
2017-09-25 14:59:34 -04:00
8f25cfa36e
r437: fixed uninialized memory on rep_len
2017-09-25 14:22:45 -04:00
81008dd371
r436: working on short reads
...
The result is mixed - lots of room for tuning
2017-09-25 14:06:29 -04:00
3bb66e1ed3
multi-seg working on toy examples
2017-09-25 13:42:04 -04:00
a742f10164
get multi-seg code ready; probably not working yet
2017-09-24 15:17:17 -04:00
Heng Li