Heng Li
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5ead86acd3
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optionally mark split hit as secondary
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2013-02-25 11:18:35 -05:00 |
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Heng Li
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85775c3384
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output multiple hits
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2013-02-24 13:23:43 -05:00 |
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Heng Li
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6bdccf2a8a
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added a bit documentation
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2013-02-24 13:09:29 -05:00 |
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Heng Li
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ee59a13109
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simplified bwamem.h
Hide mem_seed_t and mem_chain_t. Don't expose unnecessary routines.
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2013-02-24 12:17:29 -05:00 |
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Heng Li
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e613195e17
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moved some common code to bwa.{c,h}
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2013-02-23 15:30:46 -05:00 |
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Heng Li
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17c123d65a
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pring paired-end SAM
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2013-02-22 16:38:48 -05:00 |
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Heng Li
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a578688fa8
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generate multiple alignments from one chain
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2013-02-21 14:58:51 -05:00 |
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Heng Li
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54da54ffd4
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extend more seeds (and thus slower...)
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2013-02-21 12:52:00 -05:00 |
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Heng Li
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5626fe29b7
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Well, at least output sth
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2013-02-20 19:11:44 -05:00 |
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Heng Li
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688872fb1b
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code backup
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2013-02-19 00:50:39 -05:00 |
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Heng Li
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66585b7982
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code backup
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2013-02-18 16:33:06 -05:00 |
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Heng Li
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df1ff2b36e
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better and proper way to infer orinentation
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2013-02-14 12:59:32 -05:00 |
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Heng Li
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604e3d8da1
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code backup; to upgrade ksw.{c,h}
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2013-02-12 16:15:26 -05:00 |
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Heng Li
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cd0969332f
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keep track of the "parent" of a secondary
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2013-02-12 15:52:23 -05:00 |
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Heng Li
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22b79b3475
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mark primary, instead of dropping secondary
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2013-02-12 15:34:44 -05:00 |
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Heng Li
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95d18449b3
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merge bseq.{h,c} to utils.{h,c}
I do not like many small files.
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2013-02-12 10:36:15 -05:00 |
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Heng Li
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99907c98fb
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separated and improved SAM printing code
This is for the PE mode. The routines may also be useful for bwa-sw, but
probably I won't change the old code.
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2013-02-11 15:29:03 -05:00 |
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Heng Li
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59eaf650ac
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code backup
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2013-02-11 10:59:38 -05:00 |
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Heng Li
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829664d6b5
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missing identical hits; improved sub_n
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2013-02-08 17:55:35 -05:00 |
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Heng Li
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b2c7148dc9
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consider the number of suboptimal hits
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2013-02-08 17:20:44 -05:00 |
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Heng Li
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39607065e0
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allow more seeds to be seen (thus slower..)
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2013-02-08 16:56:28 -05:00 |
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Heng Li
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fdb0a7405f
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better dealing with microrepeat
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2013-02-08 14:46:57 -05:00 |
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Heng Li
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1bf1a674a8
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minor improvement to mapQ
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2013-02-08 13:43:15 -05:00 |
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Heng Li
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bfeb37c4de
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code backup
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2013-02-07 13:29:01 -05:00 |
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Heng Li
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5dc398cdef
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start to write CLI
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2013-02-07 13:13:43 -05:00 |
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Heng Li
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5a0b32bfd2
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updated to the latest kseq.h
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2013-02-06 14:38:40 -05:00 |
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Heng Li
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a9292d674d
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a bit code cleanup
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2013-02-06 13:59:32 -05:00 |
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Heng Li
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e65b2096f7
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removed useless members
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2013-02-06 12:25:49 -05:00 |
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Heng Li
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a61288c768
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separate CIGAR generation
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2013-02-05 21:49:19 -05:00 |
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Heng Li
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d6a73c9171
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chain filtering apparently working
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2013-02-05 00:17:20 -05:00 |
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Heng Li
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9d0cdb2d3c
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unfinished chain filter
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2013-02-04 17:23:06 -05:00 |
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Heng Li
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f27bd18f20
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check if every seed is included; not used for now
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2013-02-04 15:09:47 -05:00 |
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Heng Li
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5bfa45a69b
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write the mem_aln_t struct
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2013-02-04 15:02:56 -05:00 |
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Heng Li
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ba18db1a9f
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sw extension works for the simplest case
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2013-02-04 12:37:38 -05:00 |
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Heng Li
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d25a87cc50
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code backup
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2013-02-02 15:14:24 -05:00 |
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Heng Li
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00e5302219
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routine to get subsequence from 2-bit pac
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2013-02-01 16:39:50 -05:00 |
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Heng Li
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f8f3b7577a
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code cleanup; added a missing file
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2013-02-01 14:38:44 -05:00 |
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Heng Li
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620ad6e5b9
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reseed long SMEMs
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2013-02-01 14:20:38 -05:00 |
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Heng Li
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8977737460
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basic chaining working
Definitely suboptimal in a lot of corner cases...
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2013-01-31 16:26:05 -05:00 |
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Heng Li
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6c19c9640c
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code backup
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2013-01-31 15:55:22 -05:00 |
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Heng Li
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91debf412b
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move smem iterators to bwamem.{c,h}
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2013-01-31 13:59:48 -05:00 |