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Author SHA1 Message Date
Heng Li 37e627aa98 note on long cigar in README 2017-10-21 22:28:06 -04:00
Heng Li beeb806829 r526: fixed a bug when HPC is in use 
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
Heng Li be7f3c4ffe r525: fixed a bug in chaining; handle ovlp ends 2017-10-20 21:34:52 -04:00
Heng Li bd04372873 r524: reverted to bwa-mem end bonus 
and reduced the cost of clipping when filtering by identity
 2017-10-20 16:57:31 -04:00
Heng Li 15ed0712c2 r523: fixed a performance bug in ksw2_ll 
Wont' affect accuracy.
 2017-10-20 13:00:10 -04:00
Heng Li 55dcbefe87 updated text (unfinished) 2017-10-20 12:44:54 -04:00
Heng Li 8abba332ad replaced mapQ plot with sr roc 
figure legend and text to be updated later
 2017-10-19 23:43:17 -04:00
Heng Li 4683da2455 r520: added option -L to write long cigar to CG 2017-10-17 17:32:44 -04:00
Heng Li ffd953029f r519: fixed a severe bug that misses long alns 2017-10-17 15:52:36 -04:00
Heng Li 04cf4ebf5e r518: increased the default -K to 500M 
This helps multi-thread performance for ultra-long reads.
 2017-10-17 13:21:29 -04:00
Heng Li 25ffd72690 r517: replaced --print-2nd with --secondary 2017-10-17 11:41:56 -04:00
Heng Li aa2d9d4e1b r516: throw a warning if -N0 is used 2017-10-16 14:55:35 -04:00
Heng Li addb61bcb2 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.
 2017-10-16 13:58:01 -04:00
Heng Li b24c9c90c7 updated mappy and example.c 2017-10-16 11:15:07 -04:00
Heng Li 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
Heng Li e6f525edaf r512: option to filter poorly aligned reads 2017-10-16 10:38:22 -04:00
Heng Li 858213d513 r511: fixed wrong primary sam record 2017-10-12 23:02:18 -04:00
Heng Li dea3b60918 r510: fixed an off-by-1 bug for unmapped mate 2017-10-12 17:31:13 -04:00
Heng Li 7c555f9b7e r508: use two I/O threads for mapping 
-x sr applies this option by default
 2017-10-12 14:56:01 -04:00
Heng Li 2801ed9b4b r507: -K not working as is intended (#36) 2017-10-12 14:16:05 -04:00
Heng Li 27025c70a7 added evaluation scripts to README 2017-10-12 12:55:10 -04:00
Heng Li 9bafbe4e70 added Getting help and cs 2017-10-12 12:40:52 -04:00
Heng Li ce06188203 r506: fixed a memory leak 2017-10-12 10:12:22 -04:00
Heng Li 9862a75cd3 r505: a bit code simplification 2017-10-11 21:54:32 -04:00
Heng Li 3073f4a758 r504: better heuristics to reduce excessive ext 2017-10-11 21:42:11 -04:00
Heng Li ba6ddda6b0 Merge pull request #35 from mcshane/sam_fix 
fix sam output for some unmapped queries
 2017-10-11 20:09:16 -04:00
Heng Li 9364bc64d7 r501: added end_bonus to extz2 2017-10-11 09:39:41 -04:00
Heng Li 65abdb8f3c r500: temporarily disabled region trunc 
because it is causing other problems.
 2017-10-11 00:16:04 -04:00
Heng Li 7345621759 r499: end bonus working; DP region needs improve! 2017-10-11 00:14:25 -04:00
Heng Li ca632f907b r498: fixed a bug when merging like "4I5I" 2017-10-10 21:22:37 -04:00
Heng Li 6c78a980b6 r497: the previous change not working at the ends 2017-10-10 17:32:28 -04:00
Heng Li c217eecdb7 r496: avoid DP extending into another chain 
When deciding the region for DP, exclude regions in the adjacent chain
 2017-10-10 17:25:12 -04:00
Heng Li 13b66aad4d 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
 2017-10-10 11:59:44 -04:00
Heng Li 46fa520db9 r494: simpler and better SR gap filling 
Still one thing to do: left alignment
 2017-10-09 22:02:30 -04:00
Heng Li 1e53610fb4 r493: reduced calling extd2 for ungapped aln 
Still need to improve in case of 3I5M3D
 2017-10-09 21:13:34 -04:00
Heng Li 9396d9e11b r452: typo in the last commit 2017-10-09 10:05:32 -04:00
Heng Li 198849a716 r491: an ambiguous base costs the same as gap ext 2017-10-09 09:59:42 -04:00
Heng Li 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.
 2017-10-08 21:36:34 -04:00
Heng Li f9415628a8 r489: don't use approximate zdrop 
it doesn't work well
 2017-10-08 19:29:09 -04:00
Heng Li 61e56c941d r488: parameter to control max fragment length 2017-10-07 23:54:32 -04:00
Heng Li f150257a0d r487: demote "map10k"; improved README 2017-10-07 19:19:40 -04:00
Heng Li bf2d4f7aec r486: treat "U" as "T" for RNA reads (#33) 2017-10-07 18:53:25 -04:00
Heng Li 47b86e765b minor wording changes 2017-10-06 15:34:20 -04:00
Heng Li 56acf6ee28 completed README rewrite 2017-10-06 14:26:02 -04:00
Heng Li 4f6244bd4a revamped README; not finished yet 2017-10-06 13:02:25 -04:00
Heng Li c6384ed2c8 r482: increased short-read bandwidth to 100 
This has very minor effect on speed.
 2017-10-06 10:20:32 -04:00
Heng Li 2833a9c255 150bp mason2 simulation 2017-10-06 09:46:59 -04:00
Heng Li de2fcc1bf3 updated the mappy 2017-10-05 17:10:07 -04:00
Heng Li e0baf1ad54 r479: a bit code cleanup 2017-10-05 16:15:14 -04:00
Heng Li f266092699 r478: simplied useless code, a tiny bit 2017-10-05 15:56:00 -04:00
Heng Li 9c5767f9ed r477: renamed multi_seg to frag_mode 2017-10-05 15:48:17 -04:00
Heng Li ae2adf04d4 r476: multi-file fragment mode working 2017-10-05 15:39:26 -04:00
Heng Li b839758335 r475: added --cs=none; updated manpage 2017-10-05 15:27:37 -04:00
Heng Li f4a5d3a692 r474: replaced -S and --cs-no-equal with --cs 2017-10-05 15:03:03 -04:00
Heng Li 3ff6eda3a4 r473: don't count introns into blen 2017-10-05 14:37:21 -04:00
Heng Li 1a90bc8603 r472: fixed a bug when printing MAPQ/CIGAR 2017-10-05 12:46:11 -04:00
Heng Li abf2a90363 r471: all SAM features implemented; more tests! 2017-10-05 12:37:30 -04:00
Heng Li 5ab99eb26e more accurate SAM flag 2017-10-05 10:59:38 -04:00
Heng Li 7cc4f6f965 r469: first step towards PE SAM 2017-10-05 10:38:09 -04:00
Heng Li 16e6e589a8 r468: replaced ^ with ~ in cs 2017-10-04 22:17:12 -04:00
Heng Li 9aba11769c r467: added : (equal length) and ^ (intron) ops 2017-10-04 21:55:37 -04:00
Heng Li 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
Heng Li 1554149158 r465: apply option -x before other options 2017-10-04 13:52:28 -04:00
Heng Li 19c39e704f r464: fixed a bug in pairing, due to randomization 2017-10-04 13:37:40 -04:00
Heng Li 2581c44a21 r463: optionally disable secondary hits 2017-10-04 13:24:41 -04:00
Heng Li 5babf41a38 r462: SAM primary flag not properly set 2017-10-04 13:11:29 -04:00
Heng Li 2a1e738a94 r461: randomize repetitive hits 2017-10-04 13:05:18 -04:00
Heng Li cf55c84056 r460: added option --no-long-join 2017-10-04 12:08:44 -04:00
Heng Li 841763ec24 Merge branch 'master' into sr 2017-10-04 11:42:44 -04:00
Heng Li 95eb1dec36 r458: fixed wrong chr for inversion aln (#30) 2017-10-04 11:32:06 -04:00
Heng Li 0fd0f2aed1 r457: fixed a bug on parsing -f 2017-09-30 00:00:44 -04:00
Heng Li 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
Heng Li 340483821e r455: set max_occ on command line 2017-09-29 22:18:43 -04:00
Heng Li 04fb2c2ec0 r454: rechain with higher max_occ if no good chain 2017-09-29 19:24:32 -04:00
Heng Li 0d4ecd19ee r453: avoid duplicated strcmp() for ava 2017-09-28 15:52:05 -04:00
Heng Li 0c63325985 r452: fixed - -G not working with -x sr 2017-09-28 14:28:12 -04:00
Heng Li 2a554a92e9 r451: changed rep_len mapq heuristic 2017-09-28 14:23:14 -04:00
Heng Li 935a6e6064 r450: differentiate exact repeats via mapq 2017-09-27 23:51:05 -04:00
Heng Li a13691d00d eval script works with /[12] in SAM 2017-09-27 23:33:59 -04:00
Heng Li 8301222174 r448: fixed a bug when computing PE quality 2017-09-27 21:54:07 -04:00
Heng Li 9541052564 r447: paired-end mapping quality 
not as good as I would hope...
 2017-09-27 15:39:25 -04:00
Heng Li 7e0d70bfd3 r445: pair coordinate adjustment working 
Next: mapq adjustment, which will be tricky...
 2017-09-27 15:38:18 -04:00
Heng Li 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
Heng Li f611edf6f2 r443: don't filter small cm for split seg 2017-09-26 16:17:58 -04:00
Heng Li 1b1dd0cd57 r442: default max_gap to 200 in the sr mode 2017-09-26 13:31:01 -04:00
Heng Li 92ec8bd859 added the /1 or /2 suffix 2017-09-26 12:04:35 -04:00
Heng Li 55d1e4f638 r440: better chain filtering for PE reads 2017-09-26 11:03:36 -04:00
Heng Li 64c0ad6b35 r439: use splice-like chain gap cost between segs 
This improves accuracy
 2017-09-25 16:04:38 -04:00
Heng Li 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
Heng Li 8f25cfa36e r437: fixed uninialized memory on rep_len 2017-09-25 14:22:45 -04:00
Heng Li 81008dd371 r436: working on short reads 
The result is mixed - lots of room for tuning
 2017-09-25 14:06:29 -04:00
Heng Li 3bb66e1ed3 multi-seg working on toy examples 2017-09-25 13:42:04 -04:00
Heng Li a742f10164 get multi-seg code ready; probably not working yet 2017-09-24 15:17:17 -04:00
Heng Li f0951141a1 allow to read multiple files interleaved 2017-09-24 14:33:05 -04:00
Heng Li 84bbc47152 two arrays should be freed with kfree(0,) 
though in the current code, they are strictly equivalent.
 2017-09-23 10:43:22 -04:00
Heng Li 5400191097 get batch sequence reader ready for paired-end 2017-09-22 09:56:31 -04:00
Heng Li ef84e8b4e7 Merge branch 'master' into sr 2017-09-20 23:56:06 -04:00
Heng Li 1c948e0d1d added GMAP iso-seq numbers 2017-09-20 23:54:02 -04:00
Heng Li 997011458c fixed uninitialized value due to last commit 2017-09-20 15:10:48 -04:00
Heng Li 19d8eca3a1 moved array shrinking into chain_dp() 2017-09-20 14:58:57 -04:00