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Support indexed GAF #4248

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merged 24 commits into from
Apr 8, 2024
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6828f9e
implement simple chunk-merge sorting for GAFs
jmonlong Mar 25, 2023
e9c431f
fix overflow nodeid and add some progress logging
jmonlong Mar 29, 2023
060cfcb
fix comment typo
jmonlong Jul 4, 2023
0c5060b
add sorted gaf input option to vg find
jmonlong Jul 4, 2023
1493936
use more explicit var names for the gaf part
jmonlong Jul 4, 2023
423632a
use consistent indentation...
jmonlong Jul 4, 2023
e731f65
remove debug log
jmonlong Jul 4, 2023
a8e7fac
add gaf input to vg chunk (only when specifying a region or node ids)
jmonlong Jul 4, 2023
ddc9a9a
fix error triggering for gaf splitting/components
jmonlong Jul 31, 2023
39a3652
minor comments/msg updates
Jul 31, 2023
f306e4a
handle bed regions on paths that are chopped in subpaths
Aug 2, 2023
383622f
gff annotation also handle paths chopped into subpaths
jmonlong Aug 3, 2023
bb5c059
handle subrange with no end position, plus some dev tests
Aug 8, 2023
260d837
handle 2 subpath formats and regions spanning subpaths (naively)
Aug 9, 2023
e064068
save absent path to avoid querying too much
Aug 9, 2023
98ec1ef
Merge branch 'gafidx' of github.com:vgteam/vg into gafidx
Aug 9, 2023
9ee63a2
better handle regions overlapping subpaths
Aug 9, 2023
ab9b79c
simplify how chopped regions are handled and propagate to gff parser
Aug 10, 2023
9d5df77
better handle temporary files
Aug 16, 2023
ae44fca
write alignment buffers once in a while
Aug 20, 2023
73593a5
use a min-heap when mergin sorted GAF and simplify to speed up
Aug 24, 2023
d9f20c9
update htslib dep
jmonlong Sep 20, 2023
377f3f0
Merge remote-tracking branch 'origin/master' into gafidx
adamnovak Mar 26, 2024
fc59bec
Update htslib to the version with GAF indexing merged
adamnovak Mar 26, 2024
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Update htslib to the version with GAF indexing merged
adamnovak committed Mar 26, 2024
commit fc59bec26c54f8ee4e20ad2135994163f71dc893
2 changes: 1 addition & 1 deletion deps/htslib
Submodule htslib updated 213 files