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Author SHA1 Message Date
Heng Li 71e2a97a4c r180: changed -x asm5 settings 2017-07-18 00:00:36 -04:00
Heng Li 941059292e r179: changed the preset for assembly alignment 2017-07-17 22:41:46 -04:00
Heng Li 38aa66fa30 r178: fixed integer overflow in mapq calculation 2017-07-16 21:45:39 -04:00
Heng Li f42790398d fixed a band boundary bug in ksw2 2017-07-16 17:52:57 -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 cfa083a98b r172: separated PacBio and ONT read overlapping 
HPC k-mer works better for PacBio, but worse for ONT. Interesting...
 2017-07-11 15:12:35 -04:00
Heng Li 7598809577 r171: reduced log gap cost at chaining 
The cost is so large that it discards too many valid seeds without HPC k-mers.
This change may introduce false long gaps to reference mapping. We have another
mechanism mm_filter_bad_seeds() to protect against this. In addition, minimap2
is not that bad to have long gaps. Some other aligners are worse.

Still need tuning in future.
 2017-07-11 14:57:49 -04:00
Heng Li 826c8ba892 r170: added a debugging flag 
something wrong with chaining
 2017-07-11 14:47:35 -04:00
Heng Li 801bc84b01 r169: output more accurate col. 10&11 to PAF 
In r168, col.10 is smaller than what it should be. This confuses miniasm.
 2017-07-11 14:09:51 -04:00
Heng Li 782449975d r168: fixed a bug in long join: a[] not sorted 
Also added length requirement for long join and changed -g in the ava mode
 2017-07-09 12:14:20 -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 34ed85d46a optionally print the postions of long indels 2017-07-08 20:16:25 -04:00
Heng Li 2f11a63b22 script to collect alignment stats 2017-07-08 20:01:36 -04:00
Heng Li 4ee3202539 r164: unmapped read not properly flagged 2017-07-08 18:16:18 -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 3f6a0b0b5c r162: improved chaining accuracy 2017-07-08 14:29:36 -04:00
Heng Li 38b2830e18 r161: filter bad seeds; changed default -g/-r 2017-07-08 13:31:27 -04:00
Heng Li 1fee5f8edc r160: -O and -E accept two numbers 2017-07-08 11:34:52 -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 d1f518e3ca for clarity 2017-07-04 11:56:50 -04:00
Heng Li 6b584a1235 added README 2017-07-04 11:47:29 -04:00
Heng Li 8fff901e53 added test data 2017-07-04 10:56:48 -04:00
Heng Li a65e557a7c Merge branch 'dev' 2017-07-03 13:19:17 -04:00
Heng Li e07daad7ad r153: sam primary record not set sometimes 2017-07-03 13:18:57 -04:00
Heng Li 6ead8af104 Merge branch 'dev' into 'master' 
Fixed bugs when reporting secondary alignments

See merge request !1
 2017-07-03 16:17:08 +00:00
Heng Li a94bc31311 r151: documentations 2017-07-03 12:11:07 -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 696ebce66e backup; still buggy 2017-07-03 00:52:00 -04:00
Heng Li e06c342659 r146: in filtering, drop children if parent out 
This has been causing several segfaults.
 2017-07-03 00:28:12 -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 632b8638d2 r144: adjust primary aln after cigar 2017-07-02 22:43:02 -04:00
Heng Li 2b45ba7a0b r143: fixed a segfault and incorrect .parent 2017-07-02 19:56:21 -04:00
Heng Li 74d306a596 fixed bug when retaining 2ndary aln; still buggy 2017-07-02 19:08:30 -04:00
Heng Li da90b614db r141: replaced -b with -a (for SAM output) 
-b sounds like BAM. I like -a better.
 2017-07-01 16:54:59 -04:00
Heng Li 67cad9dff3 added limitations 2017-07-01 12:11:56 -04:00
Heng Li a92bd75b7b make the table fit 80 columns 2017-07-01 11:54:07 -04:00
Heng Li 02145b2166 explain option -d 2017-07-01 11:48:37 -04:00
Heng Li 3c45d84012 added license 2017-07-01 11:39:19 -04:00
Heng Li b2ce3f9ed0 get rid of two more new lines 2017-07-01 11:37:58 -04:00
Heng Li 5ebe868db5 added two more new lines 2017-07-01 11:32:49 -04:00
Heng Li cb6c277c62 removed unnecessary empty lines 
On linux, these empty lines count.
 2017-07-01 11:31:32 -04:00
Heng Li b883d132e2 no effective change 2017-07-01 11:26:23 -04:00
Heng Li 2338e887d9 finished the first draft of manpage 2017-07-01 11:25:54 -04:00
Heng Li a9f089f0aa r131: wrong EOF test; make mb_size <= batch_size 2017-07-01 09:26:09 -04:00
Heng Li d4301736b8 more manpage 2017-07-01 00:23:46 -04:00
Heng Li 41efd03d7a r129: fixed memory leak caused by qualities 2017-06-30 23:48:00 -04:00
Heng Li 10910b72d1 backup 2017-06-30 23:31:38 -04:00
Heng Li d118cafd25 added man page 2017-06-30 23:30:17 -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 d73bb28097 r125: changed CLI options 2017-06-30 19:08:47 -04:00
Heng Li b08591c7a0 r124: a bit better CLI prompt 2017-06-30 15:46:52 -04:00
Heng Li 3a5486325a r123: fixed a mem leak; more presets 2017-06-30 15:39:05 -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 08a61c3cfc r119: fixed a bug hidden by a previous bug 2017-06-30 13:27:47 -04:00
Heng Li 1a903486b9 r118: bugfix - regs unsorted before filtering 2017-06-30 12:52:28 -04:00
Heng Li 5dcd8f8965 r117: fixed a bug in logic 2017-06-30 11:52:42 -04:00
Heng Li 91e1c4d6db r116: fixed another bug caused by refactoring 2017-06-30 00:03:45 -04:00
Heng Li 52b4d8e2c9 r115: set primary tag; still buggy 2017-06-29 23:48:35 -04:00
Heng Li c4871f380c r114: make SAM output better 2017-06-29 23:08:41 -04:00
Heng Li 03267e8fa7 r113: fixed a sam header bug 2017-06-29 22:43:06 -04:00
Heng Li 11167f511b r112: output z-drop 2017-06-29 22:08:46 -04:00
Heng Li 3825feeeac r111: changed the default z-drop to 200 2017-06-29 21:37:56 -04:00
Heng Li e2b86d0332 r110: fixed a bug caused by refactoring 2017-06-29 21:12:31 -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 337c2a21cd r105: fixed a bug in repeated right ext when zdrop 2017-06-29 15:45:07 -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 d274e1b743 backup 2017-06-29 12:58:52 -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 cf703655cb optional sse4 2017-06-28 22:21:52 -04:00
Heng Li 38070e8a05 r98: fixed segfault for certain scoring 
due to unsigned comparisons between -1 and chromosome length
 2017-06-28 22:18:51 -04:00
Heng Li 5e202afb5f fixed invalid backtracking, a temporary solution 2017-06-28 18:17:57 -04:00
Heng Li a25866c25c r96: min_cnt still wrong in chaining 2017-06-28 11:03:03 -04:00
Heng Li b696d5fe5e disable kalloc in the debugging mode 2017-06-28 10:50:27 -04:00
Heng Li bf0e8199e2 r94: min_cnt is tested in a wrong way in chain 2017-06-28 10:39:27 -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 51057ab673 expose scoring 2017-06-27 21:37:25 -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 8977f07269 r88: fixed an out-of-boundary bug in ksw2 2017-06-27 14:50:31 -04:00
Heng Li 42283ef10c r87: fixed a bug in ksw2 2017-06-27 13:29:48 -04:00
Heng Li 734028f92b validate z-drop 2017-06-27 11:25:39 -04:00
Heng Li c02ff4662c r85: two-round z-drop 2017-06-27 10:36:24 -04:00
Heng Li 490a37a599 number of allocated units must be an even number 2017-06-26 23:15:30 -04:00
Heng Li 0d03a43efd don't round to power-of-2 
Because rounding wastes memory when we use power-of-2 high-water marks.
 2017-06-26 22:10:45 -04:00
Heng Li b56cd790f6 enabled kalloc (was a mistake) 
Not using kalloc leads to significant malloc overhead.
 2017-06-26 15:41:55 -04:00
Heng Li 99c57b86c5 r79: drop bad hits 2017-06-26 15:28:04 -04:00