mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 13:30:52 +00:00
f78543ee75
Refactor k-mer index building to use the new disk-based KmerSetGroupBuilder instead of the old KmerSet and FrequencyFilter approaches. This change introduces a more efficient and scalable approach to building k-mer indices by using partitioned disk storage with streaming operations. - Replace BuildKmerIndex and BuildFrequencyFilterIndex with KmerSetGroupBuilder - Add support for frequency filtering via WithMinFrequency option - Remove deprecated k-mer set persistence methods - Update CLI to use new builder approach - Add new disk-based k-mer operations (union, intersect, difference, quorum) - Introduce KDI (K-mer Delta Index) file format for efficient storage - Add K-way merge operations for combining sorted k-mer streams - Update documentation and examples to reflect new API This refactoring provides better memory usage, faster operations on large datasets, and more flexible k-mer set operations.
54 lines
1.8 KiB
Modula-2
54 lines
1.8 KiB
Modula-2
module git.metabarcoding.org/obitools/obitools4/obitools4
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go 1.23.4
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toolchain go1.24.2
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require (
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github.com/DavidGamba/go-getoptions v0.28.0
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github.com/PaesslerAG/gval v1.2.2
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github.com/barkimedes/go-deepcopy v0.0.0-20220514131651-17c30cfc62df
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github.com/buger/jsonparser v1.1.1
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github.com/chen3feng/stl4go v0.1.1
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github.com/dlclark/regexp2 v1.11.4
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github.com/goccy/go-json v0.10.3
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github.com/klauspost/pgzip v1.2.6
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github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58
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github.com/pelletier/go-toml/v2 v2.2.4
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github.com/rrethy/ahocorasick v1.0.0
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github.com/schollz/progressbar/v3 v3.13.1
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github.com/sirupsen/logrus v1.9.3
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github.com/stretchr/testify v1.8.4
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github.com/tevino/abool/v2 v2.1.0
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github.com/yuin/gopher-lua v1.1.1
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golang.org/x/exp v0.0.0-20231110203233-9a3e6036ecaa
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gonum.org/v1/gonum v0.14.0
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gopkg.in/yaml.v3 v3.0.1
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scientificgo.org/special v0.0.0
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)
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require (
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github.com/davecgh/go-spew v1.1.1 // indirect
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github.com/goombaio/orderedmap v0.0.0-20180924084748-ba921b7e2419 // indirect
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github.com/kr/pretty v0.3.1 // indirect
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github.com/kr/text v0.2.0 // indirect
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github.com/pmezard/go-difflib v1.0.0 // indirect
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github.com/rogpeppe/go-internal v1.12.0 // indirect
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)
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require (
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github.com/dsnet/compress v0.0.1
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github.com/gabriel-vasile/mimetype v1.4.3
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github.com/goombaio/orderedset v0.0.0-20180925151225-8e67b20a9b77
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github.com/klauspost/compress v1.17.2
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github.com/mattn/go-runewidth v0.0.15 // indirect
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github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
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github.com/rivo/uniseg v0.4.4 // indirect
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github.com/shopspring/decimal v1.3.1 // indirect
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github.com/ulikunitz/xz v0.5.11
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golang.org/x/net v0.35.0 // indirect
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golang.org/x/sys v0.30.0 // indirect
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golang.org/x/term v0.29.0 // indirect
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gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c
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)
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