beeb806829
r526: fixed a bug when HPC is in use
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It happened when the query HPC minimizer is longer than the reference HPC
minimizer close to the beginning of a contig. We may get a negative coordinate,
which causes an assertion failure.
2017-10-21 19:54:04 -04:00
be7f3c4ffe
r525: fixed a bug in chaining; handle ovlp ends
2017-10-20 21:34:52 -04:00
bd04372873
r524: reverted to bwa-mem end bonus
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and reduced the cost of clipping when filtering by identity
2017-10-20 16:57:31 -04:00
15ed0712c2
r523: fixed a performance bug in ksw2_ll
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Wont' affect accuracy.
2017-10-20 13:00:10 -04:00
55dcbefe87
updated text (unfinished)
2017-10-20 12:44:54 -04:00
8abba332ad
replaced mapQ plot with sr roc
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figure legend and text to be updated later
2017-10-19 23:43:17 -04:00
4683da2455
r520: added option -L to write long cigar to CG
2017-10-17 17:32:44 -04:00
ffd953029f
r519: fixed a severe bug that misses long alns
2017-10-17 15:52:36 -04:00
04cf4ebf5e
r518: increased the default -K to 500M
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This helps multi-thread performance for ultra-long reads.
2017-10-17 13:21:29 -04:00
25ffd72690
r517: replaced --print-2nd with --secondary
2017-10-17 11:41:56 -04:00
aa2d9d4e1b
r516: throw a warning if -N0 is used
2017-10-16 14:55:35 -04:00
addb61bcb2
r515: more conservative hit exclusion
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When a hit covers a long query subsequence that has not been covered by better
primary hits, this hit is more likely to become a new primary hit.
2017-10-16 13:58:01 -04:00
b24c9c90c7
updated mappy and example.c
2017-10-16 11:15:07 -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
858213d513
r511: fixed wrong primary sam record
2017-10-12 23:02:18 -04:00
dea3b60918
r510: fixed an off-by-1 bug for unmapped mate
2017-10-12 17:31:13 -04:00
7c555f9b7e
r508: use two I/O threads for mapping
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-x sr applies this option by default
2017-10-12 14:56:01 -04:00
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
Heng Li
Shane McCarthy