* Add CI job for Linux ARM64 too
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
* Add build job for Mac ARM64 too
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
* Pass "arm_neon=1 aarch64=1" when building on ARM64
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
* change aarch64 to arm64 for the Mac ARM64 check
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
---------
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
* 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>
This was an oversight affecting v2.22+. The latest minimap2 ranks hits and
estimates mapping quality with an adjusted alignment score (see the minimap2
update paper). This score however is not calculated when there is only one hit.
As a result, the ms:i tag varies depends on other sequences in the reference
genome, which is confusing. This change lets minimap2 to output the unadjusted
score at ms:i. At present, the adjusted score is not outputted.
Resolves#1146
* Added the lr:hq preset suggested by Nanopore developers (#1127)
* Fixed transition scoring. It did not work with presets.
* Cleaned up preset documentation
