Alt build - #92

Merged

jermp merged 33 commits into

May 6, 2026

Commits on Apr 10, 2026

pushed old changes made when travelling in Nepal: thinner bucket_type
jermp
committed
9007363

Commits on May 4, 2026

fixed issue with minimizers_tuples_iterator
claude
committed
54aa00b
step 7.2: stream over strings instead of random access
claude
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259b7fc
strings: stream to disk during build, read via small windows
claude
committed
63ea2bd
streaming dictionary save (no full strings in RAM at any point)
claude
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54e98eb
step 7.1: drop redundant tuples copy; point bucket_type into mmap
claude
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e5d2612
step 7.2 phase C: stream per-partition kmers from disk; external-memory MPHF
claude
committed
0301201

Commits on May 5, 2026

step 7.1 + 7.2 phase A: drop mmap; single ifstream pass
claude
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5f9ec80
remove all remaining mmap from the SSHash build path
claude
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a6ac614
strings_offsets: stream to disk during build
claude
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fe44326
spill the step-7 compact_vectors to disk; concatenate at save
claude
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27c71e8
spill the codewords + per-skew-partition MPHFs to disk
claude
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2c73e09
cap pthash mphf num_threads by --ram-limit
claude
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dddee47
mphf thread cap: only kick in when budget would actually be exceeded
claude
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e18b9b4
mphf: scale avg_partition_size to honor -t; cap only when pathological
claude
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869f901
clamp --ram-limit to a 4 GiB floor
claude
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8e4b0d8

Commits on May 6, 2026

bump pthash to claude/fix-pthash-memory-estimate-NhgTI
claude
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f68fa77
tighten ram-proportional buffer caps from ram/4 to ram/8
claude
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c550d53
bump pthash submodule to master tip a95e814
claude
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365758b
clang format
jermp
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526b64b
factor out buffered_record_stream<T>; remove duplicated read loops
claude
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b3e49c9
build: add --no-streaming-save flag for in-RAM save path
claude
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a35c364
Revert "build: add --no-streaming-save flag for in-RAM save path"
claude
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d7dc21d
finalize_stats: print total bits/kmer also in streaming-save flow
claude
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d832851
build_stats: format step timings as seconds with [sec] unit
claude
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030f1d0
remove dead bucket_type / minimizers_tuples_iterator
claude
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659b956
minor
jermp
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1d76541
always build via streaming-save; mmap the saved file for --check
claude
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033d59f
minor
jermp
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8abeb70
docs: add build-algorithm.md describing the streaming build pipeline
claude
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5aff9f7
docs(build-algorithm): use real CLI flag names (-g, -d)
claude
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730f0ad
Merge origin/master into alt-build: resolve conflict in util.hpp, bump version to 5.1.1

Copilot
and
jermp
authored
0002789
docs(build-algorithm): rephrase 'O(buffer)' as 'proportional to the buffer size'
claude
committed
f19ffcc