2801ed9b4b
r507: -K not working as is intended ( #36 )
2017-10-12 14:16:05 -04:00
27025c70a7
added evaluation scripts to README
2017-10-12 12:55:10 -04:00
9bafbe4e70
added Getting help and cs
2017-10-12 12:40:52 -04:00
ce06188203
r506: fixed a memory leak
2017-10-12 10:12:22 -04:00
9862a75cd3
r505: a bit code simplification
2017-10-11 21:54:32 -04:00
3073f4a758
r504: better heuristics to reduce excessive ext
2017-10-11 21:42:11 -04:00
ba6ddda6b0
Merge pull request #35 from mcshane/sam_fix
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fix sam output for some unmapped queries
2017-10-11 20:09:16 -04:00
9364bc64d7
r501: added end_bonus to extz2
2017-10-11 09:39:41 -04:00
5498565157
fix sam output for some unmapped queries
2017-10-11 08:46:24 +01:00
65abdb8f3c
r500: temporarily disabled region trunc
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because it is causing other problems.
2017-10-11 00:16:04 -04:00
7345621759
r499: end bonus working; DP region needs improve!
2017-10-11 00:14:25 -04:00
ca632f907b
r498: fixed a bug when merging like "4I5I"
2017-10-10 21:22:37 -04:00
6c78a980b6
r497: the previous change not working at the ends
2017-10-10 17:32:28 -04:00
c217eecdb7
r496: avoid DP extending into another chain
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When deciding the region for DP, exclude regions in the adjacent chain
2017-10-10 17:25:12 -04:00
13b66aad4d
r495: fix impropriate CIGAR
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1. Not left aligned
2. In one case, 50M24D50M becomes 24D100M. The leading D needs to be removed.
3. Avoid identical hits after DP
2017-10-10 11:59:44 -04:00
46fa520db9
r494: simpler and better SR gap filling
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Still one thing to do: left alignment
2017-10-09 22:02:30 -04:00
1e53610fb4
r493: reduced calling extd2 for ungapped aln
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Still need to improve in case of 3I5M3D
2017-10-09 21:13:34 -04:00
9396d9e11b
r452: typo in the last commit
2017-10-09 10:05:32 -04:00
198849a716
r491: an ambiguous base costs the same as gap ext
2017-10-09 09:59:42 -04:00
9fea4d16b3
r490: improved short-read extension heuristic
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Now we find the best scoring ungapped seeded segment and then extend from it.
There is no gap filling for short reads.
2017-10-08 21:36:34 -04:00
f9415628a8
r489: don't use approximate zdrop
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it doesn't work well
2017-10-08 19:29:09 -04:00
61e56c941d
r488: parameter to control max fragment length
2017-10-07 23:54:32 -04:00
f150257a0d
r487: demote "map10k"; improved README
2017-10-07 19:19:40 -04:00
bf2d4f7aec
r486: treat "U" as "T" for RNA reads ( #33 )
2017-10-07 18:53:25 -04:00
47b86e765b
minor wording changes
2017-10-06 15:34:20 -04:00
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
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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
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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
Heng Li
Shane McCarthy