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182 Commits (d1050f4eaf35c6df02cf92cf13d3d16b6b3bbc2a)

Author SHA1 Message Date
Heng Li e9dc1ce2b6 r205: when computing mapq, consider min_chain_sc 
Not doing this was a mistake.
 2017-07-26 11:34:14 -04:00
Heng Li 00c6db5073 r203: check more subopt aln if score small 2017-07-25 20:02:44 -04:00
Heng Li 71c988f6ab r188: renamed bseq* to mm_bseq* 
to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
 2017-07-19 09:26:46 -04:00
Heng Li 71e2a97a4c r180: changed -x asm5 settings 2017-07-18 00:00:36 -04:00
Heng Li b4280d186f r176: removed seedcov_ratio; changed default opt 
min_seedcov_ratio is not used
 2017-07-12 12:47:46 -04:00
Heng Li 52caf79395 r175: halved max-chain-skip in the ava mode 2017-07-12 10:42:19 -04:00
Heng Li eeeb2ffb68 r174: make max-chain-skip work 
The max-chain-skip heuristics did not work due to a bug. Without this
heuristics, chaining is too slow for long-read overlap.
 2017-07-12 10:08:06 -04:00
Heng Li 33451aba45 r173: changed the debugging output format 2017-07-11 15:23:28 -04:00
Heng Li 826c8ba892 r170: added a debugging flag 
something wrong with chaining
 2017-07-11 14:47:35 -04:00
Heng Li 1ac48556ae r167: long join threshold depends on gap 
also caught a bug for reverse strand join
 2017-07-09 10:38:51 -04:00
Heng Li 42846ce65d r163: reduced long join score requirement 
because the chaining score is generally smaller with the last few commits.
 2017-07-08 15:51:52 -04:00
Heng Li 38b2830e18 r161: filter bad seeds; changed default -g/-r 2017-07-08 13:31:27 -04:00
Heng Li cc554aee43 r159: use two-piece gap penalty 2017-07-08 10:26:00 -04:00
Heng Li 9823317e8f r158: optionally ignore base quality 2017-07-05 18:23:50 -04:00
Heng Li e07daad7ad r153: sam primary record not set sometimes 2017-07-03 13:18:57 -04:00
Heng Li b625247300 r150: mm_sync_regs() doesn't work with negative id 2017-07-03 11:36:34 -04:00
Heng Li 53c4bf5e4f r149: introduced debugging flags on CLI 2017-07-03 11:02:32 -04:00
Heng Li 2e4fd9f1d0 r148: revamped regs handling after cigar 2017-07-03 10:44:26 -04:00
Heng Li 51cfb60520 r145: changed default -p from 2 to 0.8 
For long reads, secondary alignments can be very information.
 2017-07-02 22:51:45 -04:00
Heng Li 74d306a596 fixed bug when retaining 2ndary aln; still buggy 2017-07-02 19:08:30 -04:00
Heng Li 41efd03d7a r129: fixed memory leak caused by qualities 2017-06-30 23:48:00 -04:00
Heng Li 426c2975f6 r126: filter by fraction of seed coverage 
otherwise we may get too many poor overlap mappings.
 2017-06-30 22:15:45 -04:00
Heng Li 646a746cdc r122: filter contained aln after DP extension 2017-06-30 15:23:30 -04:00
Heng Li fce87ce7bd r121: output QUAL and unmapped to SAM 2017-06-30 14:40:54 -04:00
Heng Li d11049eb32 r120: use max-scoring seg to control output 
much better now
 2017-06-30 14:21:44 -04:00
Heng Li 1a903486b9 r118: bugfix - regs unsorted before filtering 2017-06-30 12:52:28 -04:00
Heng Li 03267e8fa7 r113: fixed a sam header bug 2017-06-29 22:43:06 -04:00
Heng Li 3825feeeac r111: changed the default z-drop to 200 2017-06-29 21:37:56 -04:00
Heng Li 08cbb09fcc r109: changed the default scoring 2017-06-29 20:21:57 -04:00
Heng Li 4cd456b9ba r108: refactoring, move reg1 routines to hit.c 2017-06-29 19:44:11 -04:00
Heng Li ecedfe5788 code refactoring for mm_reg1_t 2017-06-29 19:35:38 -04:00
Heng Li cc67f1b781 compute mapq; not working for z-split yet 2017-06-29 17:52:48 -04:00
Heng Li b9075d39a8 r104: long gap patching 2017-06-29 14:54:54 -04:00
Heng Li 17944a75c2 merge into map.c 2017-06-29 14:20:14 -04:00
Heng Li c8d122bcdb backup 2017-06-29 11:11:15 -04:00
Heng Li 9fbf7e41e1 r99: report progress 2017-06-28 23:56:33 -04:00
Heng Li b696d5fe5e disable kalloc in the debugging mode 2017-06-28 10:50:27 -04:00
Heng Li bcd9b1c621 r93: fixed various small issues 2017-06-28 10:35:21 -04:00
Heng Li cdc2a1e29f r92: fixed a bug for overlapping alignment 
On the PBcR example E. coli reads, miniasm gives one circular unitig.
 2017-06-27 22:03:31 -04:00
Heng Li 533150d49d r90: revert default band width to 1000 
10000 is excessively tolerant with bad hits.
 2017-06-27 20:29:39 -04:00
Heng Li fa80177e58 r89: added minimal number of minimizer counts 2017-06-27 18:43:15 -04:00
Heng Li 99c57b86c5 r79: drop bad hits 2017-06-26 15:28:04 -04:00
Heng Li 5b614ae828 r78: fixed a split bug 2017-06-26 14:45:23 -04:00
Heng Li de54c9dac2 r77: fixed an index loading bug (offset not set) 2017-06-26 13:56:25 -04:00
Heng Li 640b1a1727 command-line option to control CIGAR output 2017-06-26 11:41:09 -04:00
Heng Li b1077ff14c sam output 2017-06-25 22:05:20 -04:00
Heng Li 39083be9ab separated formating printing 
for SAM in future; and for performance
 2017-06-25 16:13:54 -04:00
Heng Li f20d550a59 fixed the NM bug 
due to reversed CIGAR
 2017-06-25 11:24:39 -04:00
Heng Li ef5dd318ca implemented chain splitting; NOT tested!!! 2017-06-24 22:57:43 -04:00
Heng Li aa5881e7bb backup 2017-06-24 22:51:31 -04:00
Heng Li 2d8fda9586 an alternative strategy to fix for HPC 
it makes the result better, but still not quite right.
 2017-06-24 09:26:24 -04:00
Heng Li 0c274280ae output the original score 2017-06-23 22:56:50 -04:00
Heng Li 2987be288c output cigar 2017-06-23 22:53:47 -04:00
Heng Li 35b84f88c6 backup 2017-06-23 22:42:15 -04:00
Heng Li d75b5b4e8a backup; NOT working yet 2017-06-23 19:21:47 -04:00
Heng Li 990f7b0b71 backup 2017-06-23 15:13:53 -04:00
Heng Li 4ae0b46972 min_ksw_len 2017-06-23 14:38:28 -04:00
Heng Li 44cdd18de0 start to work on alignment 2017-06-23 13:44:45 -04:00
Heng Li 372698bb23 disable k-mer intersection for now 
My current focus is long-read mapping. This functionality is not needed right now.
 2017-06-11 14:13:41 -04:00
Heng Li b04e4b9215 r36: bring back primary; don't output all mappings 2017-06-08 15:28:19 -04:00
Heng Li 6c099bef89 removed some debugging code 
not necessary when we can print PAF
 2017-06-07 14:49:11 -04:00
Heng Li be9a7f4e41 removed the old print code 2017-06-07 14:24:31 -04:00
Heng Li 8ad5cfde42 output PAF 2017-06-07 14:18:32 -04:00
Heng Li c01f2dd757 fixed a bug 2017-06-07 11:40:13 -04:00
Heng Li c1c946aa67 fixed memory leaks 
though some of them are not really leaks when kalloc is in use.
 2017-06-06 21:45:55 -04:00
Heng Li e6adb673f9 fixed a stupid bug 2017-06-06 15:45:42 -04:00
Heng Li a2958a4836 minor tweaks 2017-06-06 15:31:21 -04:00
Heng Li 6d4348db44 dp chaining mostly works, but fails sometimes 
which means there are bugs that need to be fixed
 2017-06-06 14:19:50 -04:00
Heng Li 1a9fc04cf0 backup 2017-06-06 10:16:33 -04:00
Heng Li acc7382a30 backup 2017-06-04 16:09:45 -04:00
Heng Li 949d9be872 chaining with DP 2017-05-09 22:20:57 +08:00
Heng Li 2827c29b48 minor backup 2017-05-04 23:22:11 +08:00
Heng Li 10db6b0434 wrong HPC 2017-05-04 17:45:19 +08:00
Heng Li 06adabd0dc clean bill from valgrind 2017-05-04 12:44:49 +08:00
Heng Li 7b53f7aa84 chaining 2017-05-03 20:47:29 +08:00
Heng Li f2ae8eb670 mostly debugging code 2017-05-01 16:50:09 +08:00
Heng Li 2c9f1bce3e k-mer thinning apparently working 2017-04-28 18:24:45 +08:00
Heng Li 7b7fabef4d added idx_stat 2017-04-26 22:52:28 +08:00
Heng Li de367a340c compilable again 2017-04-26 19:36:46 +08:00
Heng Li 1bf3ae6752 backup 2017-04-09 15:09:39 -04:00
Heng Li 79c9478f46 backup 2017-04-09 14:59:39 -04:00
Heng Li 8c230563cc can be compiled 2017-04-07 15:56:10 -04:00