Heng Li
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42846ce65d
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r163: reduced long join score requirement
because the chaining score is generally smaller with the last few commits.
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2017-07-08 15:51:52 -04:00 |
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Heng Li
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3f6a0b0b5c
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r162: improved chaining accuracy
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2017-07-08 14:29:36 -04:00 |
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Heng Li
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38b2830e18
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r161: filter bad seeds; changed default -g/-r
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2017-07-08 13:31:27 -04:00 |
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Heng Li
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1fee5f8edc
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r160: -O and -E accept two numbers
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2017-07-08 11:34:52 -04:00 |
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Heng Li
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cc554aee43
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r159: use two-piece gap penalty
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2017-07-08 10:26:00 -04:00 |
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Heng Li
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9823317e8f
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r158: optionally ignore base quality
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2017-07-05 18:23:50 -04:00 |
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Heng Li
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e07daad7ad
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r153: sam primary record not set sometimes
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2017-07-03 13:18:57 -04:00 |
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Heng Li
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a94bc31311
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r151: documentations
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2017-07-03 12:11:07 -04:00 |
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Heng Li
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b625247300
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r150: mm_sync_regs() doesn't work with negative id
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2017-07-03 11:36:34 -04:00 |
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Heng Li
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53c4bf5e4f
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r149: introduced debugging flags on CLI
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2017-07-03 11:02:32 -04:00 |
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Heng Li
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2e4fd9f1d0
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r148: revamped regs handling after cigar
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2017-07-03 10:44:26 -04:00 |
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Heng Li
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e06c342659
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r146: in filtering, drop children if parent out
This has been causing several segfaults.
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2017-07-03 00:28:12 -04:00 |
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Heng Li
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51cfb60520
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r145: changed default -p from 2 to 0.8
For long reads, secondary alignments can be very information.
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2017-07-02 22:51:45 -04:00 |
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Heng Li
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632b8638d2
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r144: adjust primary aln after cigar
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2017-07-02 22:43:02 -04:00 |
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Heng Li
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2b45ba7a0b
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r143: fixed a segfault and incorrect .parent
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2017-07-02 19:56:21 -04:00 |
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Heng Li
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74d306a596
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fixed bug when retaining 2ndary aln; still buggy
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2017-07-02 19:08:30 -04:00 |
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Heng Li
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da90b614db
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r141: replaced -b with -a (for SAM output)
-b sounds like BAM. I like -a better.
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2017-07-01 16:54:59 -04:00 |
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Heng Li
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2338e887d9
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finished the first draft of manpage
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2017-07-01 11:25:54 -04:00 |
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Heng Li
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a9f089f0aa
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r131: wrong EOF test; make mb_size <= batch_size
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2017-07-01 09:26:09 -04:00 |
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Heng Li
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41efd03d7a
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r129: fixed memory leak caused by qualities
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2017-06-30 23:48:00 -04:00 |
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Heng Li
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426c2975f6
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r126: filter by fraction of seed coverage
otherwise we may get too many poor overlap mappings.
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2017-06-30 22:15:45 -04:00 |
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Heng Li
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d73bb28097
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r125: changed CLI options
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2017-06-30 19:08:47 -04:00 |
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Heng Li
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b08591c7a0
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r124: a bit better CLI prompt
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2017-06-30 15:46:52 -04:00 |
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Heng Li
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3a5486325a
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r123: fixed a mem leak; more presets
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2017-06-30 15:39:05 -04:00 |
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Heng Li
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646a746cdc
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r122: filter contained aln after DP extension
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2017-06-30 15:23:30 -04:00 |
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Heng Li
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fce87ce7bd
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r121: output QUAL and unmapped to SAM
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2017-06-30 14:40:54 -04:00 |
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Heng Li
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d11049eb32
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r120: use max-scoring seg to control output
much better now
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2017-06-30 14:21:44 -04:00 |
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Heng Li
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08a61c3cfc
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r119: fixed a bug hidden by a previous bug
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2017-06-30 13:27:47 -04:00 |
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Heng Li
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1a903486b9
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r118: bugfix - regs unsorted before filtering
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2017-06-30 12:52:28 -04:00 |
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Heng Li
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5dcd8f8965
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r117: fixed a bug in logic
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2017-06-30 11:52:42 -04:00 |
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Heng Li
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91e1c4d6db
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r116: fixed another bug caused by refactoring
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2017-06-30 00:03:45 -04:00 |
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Heng Li
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52b4d8e2c9
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r115: set primary tag; still buggy
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2017-06-29 23:48:35 -04:00 |
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Heng Li
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c4871f380c
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r114: make SAM output better
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2017-06-29 23:08:41 -04:00 |
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Heng Li
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03267e8fa7
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r113: fixed a sam header bug
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2017-06-29 22:43:06 -04:00 |
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Heng Li
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11167f511b
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r112: output z-drop
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2017-06-29 22:08:46 -04:00 |
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Heng Li
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3825feeeac
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r111: changed the default z-drop to 200
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2017-06-29 21:37:56 -04:00 |
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Heng Li
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e2b86d0332
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r110: fixed a bug caused by refactoring
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2017-06-29 21:12:31 -04:00 |
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Heng Li
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08cbb09fcc
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r109: changed the default scoring
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2017-06-29 20:21:57 -04:00 |
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Heng Li
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4cd456b9ba
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r108: refactoring, move reg1 routines to hit.c
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2017-06-29 19:44:11 -04:00 |
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Heng Li
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337c2a21cd
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r105: fixed a bug in repeated right ext when zdrop
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2017-06-29 15:45:07 -04:00 |
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Heng Li
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b9075d39a8
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r104: long gap patching
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2017-06-29 14:54:54 -04:00 |
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Heng Li
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9fbf7e41e1
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r99: report progress
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2017-06-28 23:56:33 -04:00 |
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Heng Li
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38070e8a05
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r98: fixed segfault for certain scoring
due to unsigned comparisons between -1 and chromosome length
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2017-06-28 22:18:51 -04:00 |
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Heng Li
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a25866c25c
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r96: min_cnt still wrong in chaining
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2017-06-28 11:03:03 -04:00 |
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Heng Li
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bf0e8199e2
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r94: min_cnt is tested in a wrong way in chain
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2017-06-28 10:39:27 -04:00 |
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Heng Li
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bcd9b1c621
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r93: fixed various small issues
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2017-06-28 10:35:21 -04:00 |
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Heng Li
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cdc2a1e29f
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r92: fixed a bug for overlapping alignment
On the PBcR example E. coli reads, miniasm gives one circular unitig.
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2017-06-27 22:03:31 -04:00 |
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Heng Li
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51057ab673
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expose scoring
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2017-06-27 21:37:25 -04:00 |
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Heng Li
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533150d49d
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r90: revert default band width to 1000
10000 is excessively tolerant with bad hits.
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2017-06-27 20:29:39 -04:00 |
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Heng Li
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fa80177e58
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r89: added minimal number of minimizer counts
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2017-06-27 18:43:15 -04:00 |