Heng Li
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aa2d9d4e1b
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r516: throw a warning if -N0 is used
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2017-10-16 14:55:35 -04:00 |
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Heng Li
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addb61bcb2
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r515: more conservative hit exclusion
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.
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2017-10-16 13:58:01 -04:00 |
|
Heng Li
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b24c9c90c7
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updated mappy and example.c
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2017-10-16 11:15:07 -04:00 |
|
Heng Li
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adf6cd7f52
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r513: merged pre- and post-cigar blen and mlen
This saves a bit memory and is cleaner.
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2017-10-16 10:55:18 -04:00 |
|
Heng Li
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e6f525edaf
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r512: option to filter poorly aligned reads
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2017-10-16 10:38:22 -04:00 |
|
Heng Li
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858213d513
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r511: fixed wrong primary sam record
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2017-10-12 23:02:18 -04:00 |
|
Heng Li
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dea3b60918
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r510: fixed an off-by-1 bug for unmapped mate
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2017-10-12 17:31:13 -04:00 |
|
Heng Li
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7c555f9b7e
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r508: use two I/O threads for mapping
-x sr applies this option by default
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2017-10-12 14:56:01 -04:00 |
|
Heng Li
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2801ed9b4b
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r507: -K not working as is intended (#36)
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2017-10-12 14:16:05 -04:00 |
|
Heng Li
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27025c70a7
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added evaluation scripts to README
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2017-10-12 12:55:10 -04:00 |
|
Heng Li
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9bafbe4e70
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added Getting help and cs
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2017-10-12 12:40:52 -04:00 |
|
Heng Li
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ce06188203
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r506: fixed a memory leak
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2017-10-12 10:12:22 -04:00 |
|
Heng Li
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9862a75cd3
|
r505: a bit code simplification
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2017-10-11 21:54:32 -04:00 |
|
Heng Li
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3073f4a758
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r504: better heuristics to reduce excessive ext
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2017-10-11 21:42:11 -04:00 |
|
Heng Li
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ba6ddda6b0
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Merge pull request #35 from mcshane/sam_fix
fix sam output for some unmapped queries
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2017-10-11 20:09:16 -04:00 |
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Heng Li
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9364bc64d7
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r501: added end_bonus to extz2
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2017-10-11 09:39:41 -04:00 |
Shane McCarthy
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5498565157
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fix sam output for some unmapped queries
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2017-10-11 08:46:24 +01:00 |
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Heng Li
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65abdb8f3c
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r500: temporarily disabled region trunc
because it is causing other problems.
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2017-10-11 00:16:04 -04:00 |
|
Heng Li
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7345621759
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r499: end bonus working; DP region needs improve!
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2017-10-11 00:14:25 -04:00 |
|
Heng Li
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ca632f907b
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r498: fixed a bug when merging like "4I5I"
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2017-10-10 21:22:37 -04:00 |
|
Heng Li
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6c78a980b6
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r497: the previous change not working at the ends
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2017-10-10 17:32:28 -04:00 |
|
Heng Li
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c217eecdb7
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r496: avoid DP extending into another chain
When deciding the region for DP, exclude regions in the adjacent chain
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2017-10-10 17:25:12 -04:00 |
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Heng Li
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13b66aad4d
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r495: fix impropriate CIGAR
1. Not left aligned
2. In one case, 50M24D50M becomes 24D100M. The leading D needs to be removed.
3. Avoid identical hits after DP
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2017-10-10 11:59:44 -04:00 |
|
Heng Li
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46fa520db9
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r494: simpler and better SR gap filling
Still one thing to do: left alignment
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2017-10-09 22:02:30 -04:00 |
|
Heng Li
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1e53610fb4
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r493: reduced calling extd2 for ungapped aln
Still need to improve in case of 3I5M3D
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2017-10-09 21:13:34 -04:00 |
|
Heng Li
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9396d9e11b
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r452: typo in the last commit
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2017-10-09 10:05:32 -04:00 |
|
Heng Li
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198849a716
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r491: an ambiguous base costs the same as gap ext
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2017-10-09 09:59:42 -04:00 |
|
Heng Li
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9fea4d16b3
|
r490: improved short-read extension heuristic
Now we find the best scoring ungapped seeded segment and then extend from it.
There is no gap filling for short reads.
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2017-10-08 21:36:34 -04:00 |
|
Heng Li
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f9415628a8
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r489: don't use approximate zdrop
it doesn't work well
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2017-10-08 19:29:09 -04:00 |
|
Heng Li
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61e56c941d
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r488: parameter to control max fragment length
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2017-10-07 23:54:32 -04:00 |
|
Heng Li
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f150257a0d
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r487: demote "map10k"; improved README
|
2017-10-07 19:19:40 -04:00 |
|
Heng Li
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bf2d4f7aec
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r486: treat "U" as "T" for RNA reads (#33)
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2017-10-07 18:53:25 -04:00 |
|
Heng Li
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47b86e765b
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minor wording changes
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2017-10-06 15:34:20 -04:00 |
|
Heng Li
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56acf6ee28
|
completed README rewrite
|
2017-10-06 14:26:02 -04:00 |
|
Heng Li
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4f6244bd4a
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revamped README; not finished yet
|
2017-10-06 13:02:25 -04:00 |
|
Heng Li
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c6384ed2c8
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r482: increased short-read bandwidth to 100
This has very minor effect on speed.
|
2017-10-06 10:20:32 -04:00 |
|
Heng Li
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2833a9c255
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150bp mason2 simulation
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2017-10-06 09:46:59 -04:00 |
|
Heng Li
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de2fcc1bf3
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updated the mappy
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2017-10-05 17:10:07 -04:00 |
|
Heng Li
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e0baf1ad54
|
r479: a bit code cleanup
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2017-10-05 16:15:14 -04:00 |
|
Heng Li
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f266092699
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r478: simplied useless code, a tiny bit
|
2017-10-05 15:56:00 -04:00 |
|
Heng Li
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9c5767f9ed
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r477: renamed multi_seg to frag_mode
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2017-10-05 15:48:17 -04:00 |
|
Heng Li
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ae2adf04d4
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r476: multi-file fragment mode working
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2017-10-05 15:39:26 -04:00 |
|
Heng Li
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b839758335
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r475: added --cs=none; updated manpage
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2017-10-05 15:27:37 -04:00 |
|
Heng Li
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f4a5d3a692
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r474: replaced -S and --cs-no-equal with --cs
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2017-10-05 15:03:03 -04:00 |
|
Heng Li
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3ff6eda3a4
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r473: don't count introns into blen
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2017-10-05 14:37:21 -04:00 |
|
Heng Li
|
1a90bc8603
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r472: fixed a bug when printing MAPQ/CIGAR
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2017-10-05 12:46:11 -04:00 |
|
Heng Li
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abf2a90363
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r471: all SAM features implemented; more tests!
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2017-10-05 12:37:30 -04:00 |
|
Heng Li
|
5ab99eb26e
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more accurate SAM flag
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2017-10-05 10:59:38 -04:00 |
|
Heng Li
|
7cc4f6f965
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r469: first step towards PE SAM
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2017-10-05 10:38:09 -04:00 |
|
Heng Li
|
16e6e589a8
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r468: replaced ^ with ~ in cs
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2017-10-04 22:17:12 -04:00 |