Commit Graph

14 Commits

Author SHA1 Message Date
Rob Patro
358a39850f Allow passing read name to mappy (#1260)
* Allow passing read name to mappy

This adds the (optional) ability to pass the read
name to the mappy `map` method.  Without the
read name, the call to `map` can sometimes give
different output than the command line version
of `minimap2` because of the way minimap uses
the hash of the read name to break ties in ordering
hits.  This can affect which / if certain
supplementary alignments are generated, and even
which / if non-primary alignments are generated.

* Pass name directly to mm_map_aux

Get rid of additional function, and always
accept the name parameter in the mm_map_aux
function (can be nullptr if not available).

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Co-authored-by: Rob Patro <rob@newton>
2024-11-15 08:51:10 -05:00
Heng Li
b0f39a1a61 r823: mappy to index a single sequence 2018-08-05 20:57:05 -04:00
Heng Li
ff9917a1c4 r819: mappy to support cs/MD 2018-07-24 23:29:55 -04:00
Hyeshik Chang
c92a6866f3 Release the GIL to allow native Python threading. 2018-07-05 08:00:27 -04:00
Heng Li
7938ed4893 fixed two mappy warnings 2018-03-26 15:12:54 -04:00
Heng Li
96b132c97d fixed a bug/typo in Aligner.seq() (#126) 2018-03-08 19:12:12 -05:00
Heng Li
24a4808826 r718: retrieve sequence from the index 2018-02-23 10:18:26 -05:00
Heng Li
29ed675ee5 bugfix: in-place revcomp() not working 2018-02-20 11:05:54 -05:00
Heng Li
7dc7097208 added reverse complement 2018-02-20 09:41:25 -05:00
Heng Li
46d6349af4 r670: added PE support to mappy
and minor code cleanup
2018-01-31 11:33:08 -05:00
Heng Li
b24c9c90c7 updated mappy and example.c 2017-10-16 11:15:07 -04:00
Heng Li
5715c423ff exposed timer and verbose-level to mappy 2017-09-17 15:21:36 -04:00
Heng Li
c8a019fae8 exposed fasta/q reader to mappy 2017-09-17 14:41:59 -04:00
Heng Li
d5012a1b17 this is embarrassing: rename again to mappy 2017-09-17 00:05:30 -04:00