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Merged
jermp merged 115 commits into from
Dec 19, 2025
Merged

Towards v5 #84

jermp merged 115 commits into from
Dec 19, 2025

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@jermp
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@jermp jermp commented Dec 19, 2025

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jermp added 30 commits September 3, 2025 10:41
@jermp
Merge pull request #80 from jermp/master
80bf43a 
synch
@jermp
some comments on random lookup benchmark
b042476
@jermp
another comment on random lookup benchmark
5a47677
@jermp
some results on random lookup benchmark
41071fe
@jermp
updated pthash; simplified hash utils
e894045
@jermp
updated hash utils
21c2e85
@jermp
tripartition of offsets
d0e39db
@jermp
fix
550dbd9
@jermp
using 32-bit words for buckets.start_lists_of_size
80c9d00
@jermp
lookup for canonical indexes
a0140aa
@jermp
a note on presence of minimizers when lookup is resolved via the skew…
34af717 
… index
@jermp
fixed constants for skew index; merge parse and skew index construction
42c3d1d
@jermp
new results taken on 14/09/25: slightly faster construction, faster q…
c49df82 
…ueries (for a tiny space increase)
@jermp
new results.png
2c2ccc0
@jermp
new results.png
7c2e9c2
@jermp
a note on SIMD for encoding in dictionary::lookup; optimized string_t…
2155fff 
…o_uint_kmer by setting chars rather than appending
@jermp
a note about loop-unrolling in string_to_uint_kmer
c907f6d
@jermp
removed useless line
041d6d5
@jermp
minor fix to num. partitions in skew index; better access
c716fe7
@jermp
use a bits::compact_vector for (iteration to be fixed)
1ec6110
@jermp
updated external/bits
bbcc2b6
@jermp
updated external/bits and using bits::endpoints_sequence
27d8b72
@jermp
added missing include for compilation on Linux
6b48d47
@jermp
added missing include for compilation on Linux
dd1a7d2
@jermp
results 22-09-25 for k=31
053f012
@jermp
a note in readme
a972335
@jermp
perf lookup by list size
cfc22a2
@jermp
updated results to 22/09/25
3c698d7
@jermp
added endpoints.hpp
43dd436
@jermp
minor
4390b13
jermp added 29 commits November 6, 2025 23:21
@jermp
bench.py
9219105
@jermp
build.py
3e01643
@jermp
deleted old scripts
d5fb57c
@jermp
fix build.py script
2b751b2
@jermp
fix build.py script
bd8be44
@jermp
fix script
8c8562a
@jermp
updated essentials; fixed script
eefc24e
@jermp
fix streaming query multiline fasta
efc3212
@jermp
more stats to json
b7f815f
@jermp
bench results 10/11/25
2e6c05b
@jermp
updated results; better streaming query script
99900cb
@jermp
different query file for SE
c4218d1
@jermp
results updated
0502751
@jermp
benchmarks subfolder refactored
71a6a93
@jermp
print version number in main tool
98ee7a8
@jermp
a note on benchmarks
3ed53ad
@jermp
minor
4365223
@jermp
sbwt results for k=63
c769e05
@jermp
prefetching does not actually help but writing offsets to an array fi…
8c6ac62 
…rst it does
@jermp
added results for sshash-v3 to compare against
6f225a2
@jermp
removed empty json files
b59a3e4
@jermp
minor name cleanup
32fd510
@jermp
minor name cleanup
de450db
@jermp
removed some old comments
ad0cac9
@jermp
README UPDATED
1fbb593
@jermp
Merge branch 'master' into bench
4d9786f
@jermp
resolved some conflicts for merging into master
ae61108
@jermp
resolved some conflicts for merging into master
63f5927
@jermp
removed some old comments
aa95d7f
@jermp jermp merged commit 05a2626 into master Dec 19, 2025
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