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  • adf6cd7f52 r513: merged pre- and post-cigar blen and mlen Heng Li 2017-10-16 10:55:18 -0400
  • e6f525edaf r512: option to filter poorly aligned reads Heng Li 2017-10-16 10:38:22 -0400
  • 858213d513 r511: fixed wrong primary sam record Heng Li 2017-10-12 23:02:18 -0400
  • dea3b60918 r510: fixed an off-by-1 bug for unmapped mate Heng Li 2017-10-12 17:31:13 -0400
  • 7c555f9b7e r508: use two I/O threads for mapping Heng Li 2017-10-12 14:56:01 -0400
  • 2801ed9b4b r507: -K not working as is intended (#36) Heng Li 2017-10-12 14:16:05 -0400
  • 27025c70a7 added evaluation scripts to README Heng Li 2017-10-12 12:55:10 -0400
  • 9bafbe4e70 added Getting help and cs Heng Li 2017-10-12 12:40:52 -0400
  • ce06188203 r506: fixed a memory leak Heng Li 2017-10-12 10:12:22 -0400
  • 9862a75cd3 r505: a bit code simplification Heng Li 2017-10-11 21:54:32 -0400
  • 3073f4a758 r504: better heuristics to reduce excessive ext Heng Li 2017-10-11 21:42:11 -0400
  • ba6ddda6b0 Merge pull request #35 from mcshane/sam_fix Heng Li 2017-10-11 20:09:16 -0400
  • 9364bc64d7 r501: added end_bonus to extz2 Heng Li 2017-10-11 09:39:41 -0400
  • 5498565157 fix sam output for some unmapped queries Shane McCarthy 2017-10-11 08:46:24 +0100
  • 65abdb8f3c r500: temporarily disabled region trunc Heng Li 2017-10-11 00:16:04 -0400
  • 7345621759 r499: end bonus working; DP region needs improve! Heng Li 2017-10-11 00:14:25 -0400
  • ca632f907b r498: fixed a bug when merging like "4I5I" Heng Li 2017-10-10 21:22:37 -0400
  • 6c78a980b6 r497: the previous change not working at the ends Heng Li 2017-10-10 17:32:28 -0400
  • c217eecdb7 r496: avoid DP extending into another chain Heng Li 2017-10-10 17:25:12 -0400
  • 13b66aad4d r495: fix impropriate CIGAR Heng Li 2017-10-10 11:59:44 -0400
  • 46fa520db9 r494: simpler and better SR gap filling Heng Li 2017-10-09 22:02:30 -0400
  • 1e53610fb4 r493: reduced calling extd2 for ungapped aln Heng Li 2017-10-09 21:13:34 -0400
  • 9396d9e11b r452: typo in the last commit Heng Li 2017-10-09 10:05:32 -0400
  • 198849a716 r491: an ambiguous base costs the same as gap ext Heng Li 2017-10-09 09:59:42 -0400
  • 9fea4d16b3 r490: improved short-read extension heuristic Heng Li 2017-10-08 21:36:34 -0400
  • f9415628a8 r489: don't use approximate zdrop Heng Li 2017-10-08 19:29:09 -0400
  • 61e56c941d r488: parameter to control max fragment length Heng Li 2017-10-07 23:54:32 -0400
  • f150257a0d r487: demote "map10k"; improved README Heng Li 2017-10-07 19:19:40 -0400
  • bf2d4f7aec r486: treat "U" as "T" for RNA reads (#33) Heng Li 2017-10-07 18:53:25 -0400
  • 47b86e765b minor wording changes Heng Li 2017-10-06 15:34:20 -0400
  • 56acf6ee28 completed README rewrite Heng Li 2017-10-06 14:26:02 -0400
  • 4f6244bd4a revamped README; not finished yet Heng Li 2017-10-06 13:02:25 -0400
  • c6384ed2c8 r482: increased short-read bandwidth to 100 Heng Li 2017-10-06 10:20:32 -0400
  • 2833a9c255 150bp mason2 simulation Heng Li 2017-10-06 09:46:59 -0400
  • de2fcc1bf3 updated the mappy Heng Li 2017-10-05 17:10:07 -0400
  • e0baf1ad54 r479: a bit code cleanup Heng Li 2017-10-05 16:15:14 -0400
  • f266092699 r478: simplied useless code, a tiny bit Heng Li 2017-10-05 15:56:00 -0400
  • 9c5767f9ed r477: renamed multi_seg to frag_mode Heng Li 2017-10-05 15:48:17 -0400
  • ae2adf04d4 r476: multi-file fragment mode working Heng Li 2017-10-05 15:39:26 -0400
  • b839758335 r475: added --cs=none; updated manpage Heng Li 2017-10-05 15:27:37 -0400
  • f4a5d3a692 r474: replaced -S and --cs-no-equal with --cs Heng Li 2017-10-05 15:03:03 -0400
  • 3ff6eda3a4 r473: don't count introns into blen Heng Li 2017-10-05 14:37:21 -0400
  • 1a90bc8603 r472: fixed a bug when printing MAPQ/CIGAR Heng Li 2017-10-05 12:46:11 -0400
  • abf2a90363 r471: all SAM features implemented; more tests! Heng Li 2017-10-05 12:37:30 -0400
  • 5ab99eb26e more accurate SAM flag Heng Li 2017-10-05 10:59:38 -0400
  • 7cc4f6f965 r469: first step towards PE SAM Heng Li 2017-10-05 10:38:09 -0400
  • 16e6e589a8 r468: replaced ^ with ~ in cs Heng Li 2017-10-04 22:17:12 -0400
  • 9aba11769c r467: added : (equal length) and ^ (intron) ops Heng Li 2017-10-04 21:55:37 -0400
  • 7d50e646dd r466: detect multi-part index more smartly Heng Li 2017-10-04 17:32:58 -0400
  • 1554149158 r465: apply option -x before other options Heng Li 2017-10-04 13:52:28 -0400
  • 19c39e704f r464: fixed a bug in pairing, due to randomization Heng Li 2017-10-04 13:37:40 -0400
  • 2581c44a21 r463: optionally disable secondary hits Heng Li 2017-10-04 13:24:19 -0400
  • 5babf41a38 r462: SAM primary flag not properly set Heng Li 2017-10-04 13:11:29 -0400
  • 2a1e738a94 r461: randomize repetitive hits Heng Li 2017-10-04 13:05:18 -0400
  • cf55c84056 r460: added option --no-long-join Heng Li 2017-10-04 12:08:44 -0400
  • 841763ec24 Merge branch 'master' into sr Heng Li 2017-10-04 11:42:44 -0400
  • 95eb1dec36 r458: fixed wrong chr for inversion aln (#30) Heng Li 2017-10-04 11:32:06 -0400
  • 0fd0f2aed1 r457: fixed a bug on parsing -f Heng Li 2017-09-30 00:00:44 -0400
  • ee9b2773a8 r456: min chain score should >k-mer length Heng Li 2017-09-29 22:33:55 -0400
  • 340483821e r455: set max_occ on command line Heng Li 2017-09-29 22:18:43 -0400
  • 04fb2c2ec0 r454: rechain with higher max_occ if no good chain Heng Li 2017-09-29 19:24:32 -0400
  • 0d4ecd19ee r453: avoid duplicated strcmp() for ava Heng Li 2017-09-28 15:52:05 -0400
  • 0c63325985 r452: fixed - -G not working with -x sr Heng Li 2017-09-28 14:28:12 -0400
  • 2a554a92e9 r451: changed rep_len mapq heuristic Heng Li 2017-09-28 14:23:14 -0400
  • 935a6e6064 r450: differentiate exact repeats via mapq Heng Li 2017-09-27 23:51:05 -0400
  • a13691d00d eval script works with /[12] in SAM Heng Li 2017-09-27 23:33:59 -0400
  • 8301222174 r448: fixed a bug when computing PE quality Heng Li 2017-09-27 21:54:07 -0400
  • 9541052564 r447: paired-end mapping quality Heng Li 2017-09-27 15:39:25 -0400
  • 7e0d70bfd3 r445: pair coordinate adjustment working Heng Li 2017-09-27 14:33:36 -0400
  • a349d85280 r444: changed the way orientation is specified Heng Li 2017-09-27 12:33:10 -0400
  • f611edf6f2 r443: don't filter small cm for split seg Heng Li 2017-09-26 16:17:58 -0400
  • 1b1dd0cd57 r442: default max_gap to 200 in the sr mode Heng Li 2017-09-26 13:31:01 -0400
  • 92ec8bd859 added the /1 or /2 suffix Heng Li 2017-09-26 12:04:35 -0400
  • 55d1e4f638 r440: better chain filtering for PE reads Heng Li 2017-09-26 11:03:36 -0400
  • 64c0ad6b35 r439: use splice-like chain gap cost between segs Heng Li 2017-09-25 16:04:38 -0400
  • 9538c985aa r438: fixed a rare case that leads to missing hits Heng Li 2017-09-25 14:59:34 -0400
  • 8f25cfa36e r437: fixed uninialized memory on rep_len Heng Li 2017-09-25 14:22:45 -0400
  • 81008dd371 r436: working on short reads Heng Li 2017-09-25 14:06:29 -0400
  • 3bb66e1ed3 multi-seg working on toy examples Heng Li 2017-09-25 13:42:04 -0400
  • a742f10164 get multi-seg code ready; probably not working yet Heng Li 2017-09-24 15:17:17 -0400
  • f0951141a1 allow to read multiple files interleaved Heng Li 2017-09-24 14:33:05 -0400
  • 84bbc47152 two arrays should be freed with kfree(0,) Heng Li 2017-09-23 10:43:22 -0400
  • 5400191097 get batch sequence reader ready for paired-end Heng Li 2017-09-22 09:56:31 -0400
  • ef84e8b4e7 Merge branch 'master' into sr Heng Li 2017-09-20 23:56:06 -0400
  • 1c948e0d1d added GMAP iso-seq numbers Heng Li 2017-09-20 23:54:02 -0400
  • 997011458c fixed uninitialized value due to last commit Heng Li 2017-09-20 15:10:48 -0400
  • 19d8eca3a1 moved array shrinking into chain_dp() Heng Li 2017-09-20 14:58:57 -0400
  • 9943e5fdd0 backup Heng Li 2017-09-20 14:35:46 -0400
  • 5b39a1b34b Merge branch 'master' into sr Heng Li 2017-09-20 12:24:08 -0400
  • e3b5802b2e r424: reduce memory for long query seqs Heng Li 2017-09-20 12:22:13 -0400
  • 03d6894517 backup Heng Li 2017-09-20 11:47:46 -0400
  • 645db3350e Merge branch 'master' into sr Heng Li 2017-09-20 11:15:14 -0400
  • 75e6bbc9f6 r421: removed the MM_F_SPLICE_BOTH mode Heng Li 2017-09-20 11:11:53 -0400
  • 7a9b4db874 replaced --approx-ext with --sr Heng Li 2017-09-20 10:51:18 -0400
  • 4979e66ff0 Merge branch 'master' into sr Heng Li 2017-09-20 10:20:31 -0400
  • a686461e83 added github downloads counts Heng Li 2017-09-20 10:11:58 -0400
  • fd14618e61 no effective changes Heng Li 2017-09-20 10:11:05 -0400
  • 5caadc28b4 Merge branch 'master' into sr Heng Li 2017-09-19 22:31:14 -0400
  • 56014ba3db avoid assertion failure given 0-length reads Heng Li 2017-09-19 22:30:32 -0400
  • b99c22840f r414: avoid assertion failure for 0-length reads Heng Li 2017-09-19 22:21:27 -0400