+ obiskio: add binary I/O with LRU pool and compression
- Add new obiskio crate for high-performance SuperKmer serialization/deserialization - Implement binary codec with 2-bit packed sequence encoding and raw header format (32 bits) - Add transparent compression support via niffler: Zstd, Gzip/Bgzf/Lz4 - Implement SKFilePool with LRU-based fd management, max-concurrent-fd limiting (75% of ulimit) - Add SKFileWriter with batched writes, configurable flush threshold (8 KiB default), and two-phase locking - Add SKFileReader with sequential access, LRU recovery via reopen_and_seek() + New obikpartitionner crate: basic header/seq handling for binary super-kmer format - Bump niffler from 2.7 to v3, add dependencies: allocator-api2, bitflags(>=1), errno/fastrand/rustix/tempfile/lru/hashbrown/bzip2/thiserror - Update workspace members to include obikpartitionner andobiskio
This commit is contained in:
Eric Coissac
Generated
+167
-4
@@ -17,6 +17,12 @@ dependencies = [
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"memchr",
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"memchr",
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]
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]
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name = "allocator-api2"
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version = "0.2.21"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "683d7910e743518b0e34f1186f92494becacb047c7b6bf616c96772180fef923"
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[[package]]
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name = "anes"
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name = "anes"
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version = "0.2.1"
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version = "0.2.1"
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@@ -85,6 +91,24 @@ version = "0.22.1"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6"
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checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6"
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[[package]]
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name = "bgzip"
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version = "0.3.1"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "b64fd8980fb64af5951bc05de7772b598150a6f7eac42ec17f73e8489915f99b"
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dependencies = [
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"flate2",
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"log",
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"rayon",
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"thiserror 1.0.69",
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]
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[[package]]
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name = "bitflags"
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version = "2.11.1"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "c4512299f36f043ab09a583e57bceb5a5aab7a73db1805848e8fef3c9e8c78b3"
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[[package]]
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name = "bitvec"
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name = "bitvec"
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version = "1.0.1"
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version = "1.0.1"
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@@ -131,6 +155,15 @@ dependencies = [
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"libc",
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"libc",
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]
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]
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[[package]]
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name = "bzip2"
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version = "0.5.2"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "49ecfb22d906f800d4fe833b6282cf4dc1c298f5057ca0b5445e5c209735ca47"
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dependencies = [
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"bzip2-sys",
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]
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name = "bzip2-sys"
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name = "bzip2-sys"
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version = "0.1.13+1.0.8"
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version = "0.1.13+1.0.8"
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@@ -333,6 +366,28 @@ version = "1.15.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "48c757948c5ede0e46177b7add2e67155f70e33c07fea8284df6576da70b3719"
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checksum = "48c757948c5ede0e46177b7add2e67155f70e33c07fea8284df6576da70b3719"
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[[package]]
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name = "equivalent"
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version = "1.0.2"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "877a4ace8713b0bcf2a4e7eec82529c029f1d0619886d18145fea96c3ffe5c0f"
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name = "errno"
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version = "0.3.14"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "39cab71617ae0d63f51a36d69f866391735b51691dbda63cf6f96d042b63efeb"
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dependencies = [
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"libc",
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"windows-sys 0.61.2",
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]
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name = "fastrand"
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version = "2.4.1"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "9f1f227452a390804cdb637b74a86990f2a7d7ba4b7d5693aac9b4dd6defd8d6"
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name = "find-msvc-tools"
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name = "find-msvc-tools"
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version = "0.1.9"
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version = "0.1.9"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1"
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checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1"
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name = "foldhash"
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version = "0.1.5"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "d9c4f5dac5e15c24eb999c26181a6ca40b39fe946cbe4c263c7209467bc83af2"
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name = "form_urlencoded"
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name = "form_urlencoded"
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version = "1.2.2"
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version = "1.2.2"
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"zerocopy",
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"zerocopy",
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]
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]
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name = "hashbrown"
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version = "0.15.5"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "9229cfe53dfd69f0609a49f65461bd93001ea1ef889cd5529dd176593f5338a1"
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dependencies = [
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"allocator-api2",
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"equivalent",
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"foldhash",
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]
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name = "heck"
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name = "heck"
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version = "0.5.0"
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version = "0.5.0"
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@@ -586,6 +658,12 @@ dependencies = [
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"pkg-config",
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"pkg-config",
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]
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]
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name = "linux-raw-sys"
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version = "0.12.1"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "32a66949e030da00e8c7d4434b251670a91556f4144941d37452769c25d58a53"
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name = "litemap"
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name = "litemap"
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version = "0.8.2"
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version = "0.8.2"
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@@ -598,6 +676,15 @@ version = "0.4.29"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "5e5032e24019045c762d3c0f28f5b6b8bbf38563a65908389bf7978758920897"
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checksum = "5e5032e24019045c762d3c0f28f5b6b8bbf38563a65908389bf7978758920897"
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name = "lru"
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version = "0.12.5"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "234cf4f4a04dc1f57e24b96cc0cd600cf2af460d4161ac5ecdd0af8e1f3b2a38"
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dependencies = [
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"hashbrown",
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]
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name = "matchers"
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name = "matchers"
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version = "0.2.0"
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version = "0.2.0"
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@@ -629,11 +716,26 @@ version = "2.7.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "9e84f25af5326bacf3cbc3b9d2586d096426b10c889050cab891f89c9cb65932"
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checksum = "9e84f25af5326bacf3cbc3b9d2586d096426b10c889050cab891f89c9cb65932"
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dependencies = [
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dependencies = [
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"bzip2",
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"bzip2 0.4.4",
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"cfg-if",
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"cfg-if",
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"flate2",
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"flate2",
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"liblzma",
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"liblzma",
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"thiserror",
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"thiserror 2.0.18",
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"zstd",
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]
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name = "niffler"
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version = "3.0.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "62d3115cc93dac9fabdfd25f7d4fda51ad4a959fb4667d39af20f70bddfb3574"
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dependencies = [
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"bgzip",
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"bzip2 0.5.2",
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"cfg-if",
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"liblzma",
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"zstd",
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"zstd",
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]
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]
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"obiskbuilder",
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"obiskbuilder",
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]
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]
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name = "obikpartitionner"
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version = "0.1.0"
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name = "obikrope"
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name = "obikrope"
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version = "0.1.0"
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version = "0.1.0"
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@@ -704,7 +810,7 @@ name = "obiread"
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version = "0.1.0"
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version = "0.1.0"
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dependencies = [
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dependencies = [
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"infer",
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"infer",
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"niffler",
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"niffler 2.7.0",
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"obikseq",
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"obikseq",
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]
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]
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name = "obiskio"
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version = "0.1.0"
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dependencies = [
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"lru",
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]
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name = "once_cell"
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name = "once_cell"
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version = "1.21.4"
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version = "1.21.4"
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"windows-sys 0.52.0",
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"windows-sys 0.52.0",
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]
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]
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name = "rustix"
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version = "1.1.4"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "b6fe4565b9518b83ef4f91bb47ce29620ca828bd32cb7e408f0062e9930ba190"
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dependencies = [
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"bitflags",
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"libc",
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"linux-raw-sys",
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]
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version = "0.23.38"
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version = "0.23.38"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "55937e1799185b12863d447f42597ed69d9928686b8d88a1df17376a097d8369"
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checksum = "55937e1799185b12863d447f42597ed69d9928686b8d88a1df17376a097d8369"
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name = "tempfile"
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version = "3.27.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "32497e9a4c7b38532efcdebeef879707aa9f794296a4f0244f6f69e9bc8574bd"
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dependencies = [
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"fastrand",
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"getrandom 0.3.4",
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"once_cell",
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]
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name = "thiserror"
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version = "1.0.69"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "b6aaf5339b578ea85b50e080feb250a3e8ae8cfcdff9a461c9ec2904bc923f52"
|
||||||
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dependencies = [
|
||||||
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"thiserror-impl 1.0.69",
|
||||||
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]
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||||||
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[[package]]
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[[package]]
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name = "thiserror"
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name = "thiserror"
|
||||||
version = "2.0.18"
|
version = "2.0.18"
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||||
checksum = "4288b5bcbc7920c07a1149a35cf9590a2aa808e0bc1eafaade0b80947865fbc4"
|
checksum = "4288b5bcbc7920c07a1149a35cf9590a2aa808e0bc1eafaade0b80947865fbc4"
|
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dependencies = [
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dependencies = [
|
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"thiserror-impl",
|
"thiserror-impl 2.0.18",
|
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]
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name = "thiserror-impl"
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version = "1.0.69"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "4fee6c4efc90059e10f81e6d42c60a18f76588c3d74cb83a0b242a2b6c7504c1"
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dependencies = [
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"proc-macro2",
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"quote",
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"syn",
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]
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+1
-1
@@ -1,3 +1,3 @@
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[workspace]
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[workspace]
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resolver = "3"
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resolver = "3"
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members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline"]
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members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartitionner","obiskio"]
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@@ -0,0 +1,6 @@
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name = "obikpartitionner"
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version = "0.1.0"
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edition = "2024"
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[dependencies]
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@@ -0,0 +1,3 @@
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mod limits;
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pub use limits::max_concurrent_files;
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@@ -0,0 +1,150 @@
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use niffler::compression::{Format, Level, from_reader, from_writer};
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use std::fs::File;
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use std::io::{self, BufReader, BufWriter, Read, Write};
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use std::path::Path;
|
||||||
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|
||||||
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// ---------- Format binaire d'un super‑kmer (encodage 2 bits) ----------
|
||||||
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pub struct SuperKmerHeader(u32);
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|
||||||
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impl SuperKmerHeader {
|
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pub fn seq_len(&self) -> usize {
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let seql = (self.0 & 0xFF) as u8;
|
||||||
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if seql == 0 { 256 } else { seql as usize }
|
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}
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pub fn to_bits(&self) -> u32 {
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self.0
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}
|
||||||
|
pub fn from_bits(bits: u32) -> Self {
|
||||||
|
Self(bits)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
pub struct SuperKmer {
|
||||||
|
pub header: SuperKmerHeader,
|
||||||
|
pub seq: Box<[u8]>, // déjà encodée en 2 bits par base
|
||||||
|
}
|
||||||
|
|
||||||
|
impl SuperKmer {
|
||||||
|
/// Écrit ce super‑kmer dans un écrivain binaire (non compressé).
|
||||||
|
pub fn write_raw<W: Write>(&self, w: &mut W) -> io::Result<()> {
|
||||||
|
w.write_all(&self.header.to_bits().to_le_bytes())?;
|
||||||
|
w.write_all(&self.seq)?;
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Lit un super‑kmer depuis un lecteur binaire (non compressé).
|
||||||
|
/// Retourne `None` si EOF.
|
||||||
|
pub fn read_raw<R: Read>(r: &mut R, buf_seq: &mut Vec<u8>) -> io::Result<Option<Self>> {
|
||||||
|
let mut header_bytes = [0u8; 4];
|
||||||
|
if let Err(e) = r.read_exact(&mut header_bytes) {
|
||||||
|
return if e.kind() == io::ErrorKind::UnexpectedEof {
|
||||||
|
Ok(None)
|
||||||
|
} else {
|
||||||
|
Err(e)
|
||||||
|
};
|
||||||
|
}
|
||||||
|
let header = SuperKmerHeader::from_bits(u32::from_le_bytes(header_bytes));
|
||||||
|
let len_bytes = (header.seq_len() + 3) / 4; // nombre d'octets encodés
|
||||||
|
buf_seq.clear();
|
||||||
|
buf_seq.resize(len_bytes, 0);
|
||||||
|
r.read_exact(buf_seq)?;
|
||||||
|
let seq = buf_seq.clone().into_boxed_slice();
|
||||||
|
Ok(Some(SuperKmer { header, seq }))
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// ---------- PartitionManager avec compression (via niffler) ----------
|
||||||
|
pub enum CompressionFormat {
|
||||||
|
Gzip, // .gz
|
||||||
|
Zstd, // .zst
|
||||||
|
Lz4, // .lz4
|
||||||
|
Bgzf, // .bgzf (indexable par blocs)
|
||||||
|
None, // pas de compression
|
||||||
|
}
|
||||||
|
|
||||||
|
impl CompressionFormat {
|
||||||
|
/// Infère le format à partir de l'extension du fichier.
|
||||||
|
pub fn from_extension(path: &Path) -> Option<Self> {
|
||||||
|
match path.extension()?.to_str()? {
|
||||||
|
"gz" => Some(CompressionFormat::Gzip),
|
||||||
|
"zst" => Some(CompressionFormat::Zstd),
|
||||||
|
"lz4" => Some(CompressionFormat::Lz4),
|
||||||
|
"bgzf" => Some(CompressionFormat::Bgzf),
|
||||||
|
"raw" => Some(CompressionFormat::None),
|
||||||
|
_ => None,
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Extension de fichier recommandée.
|
||||||
|
pub fn extension(&self) -> &'static str {
|
||||||
|
match self {
|
||||||
|
CompressionFormat::Gzip => "gz",
|
||||||
|
CompressionFormat::Zstd => "zst",
|
||||||
|
CompressionFormat::Lz4 => "lz4",
|
||||||
|
CompressionFormat::Bgzf => "bgzf",
|
||||||
|
CompressionFormat::None => "raw",
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
pub struct PartitionWriter {
|
||||||
|
writer: Box<dyn Write + Send>, // le flux compressé
|
||||||
|
// buffer interne pour réutiliser les écritures (optionnel)
|
||||||
|
}
|
||||||
|
|
||||||
|
impl PartitionWriter {
|
||||||
|
/// Ouvre un fichier en écriture avec la compression demandée.
|
||||||
|
pub fn create(path: &Path, format: CompressionFormat) -> io::Result<Self> {
|
||||||
|
let file = File::create(path)?;
|
||||||
|
const DEFAULT_LEVEL: Level = Level::Default; // peut être ajusté
|
||||||
|
let writer: Box<dyn Write + Send> = match format {
|
||||||
|
CompressionFormat::Gzip => Box::new(from_writer(file, Format::Gzip, DEFAULT_LEVEL)?),
|
||||||
|
CompressionFormat::Zstd => Box::new(from_writer(file, Format::Zstd, DEFAULT_LEVEL)?),
|
||||||
|
CompressionFormat::Lz4 => Box::new(from_writer(file, Format::Lz4, DEFAULT_LEVEL)?),
|
||||||
|
CompressionFormat::Bgzf => Box::new(from_writer(file, Format::Bgzf, DEFAULT_LEVEL)?),
|
||||||
|
CompressionFormat::None => Box::new(BufWriter::new(file)),
|
||||||
|
};
|
||||||
|
Ok(PartitionWriter { writer })
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Écrit un super‑kmer (non compressé individuellement) dans le flux compressé.
|
||||||
|
pub fn write_kmer(&mut self, kmer: &SuperKmer) -> io::Result<()> {
|
||||||
|
kmer.write_raw(&mut self.writer)
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Flush final.
|
||||||
|
pub fn finish(mut self) -> io::Result<()> {
|
||||||
|
self.writer.flush()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
pub struct PartitionReader {
|
||||||
|
reader: Box<dyn Read + Send>,
|
||||||
|
seq_buf: Vec<u8>, // réutilisation pour les séquences
|
||||||
|
}
|
||||||
|
|
||||||
|
impl PartitionReader {
|
||||||
|
/// Ouvre un fichier en lecture. Détecte automatiquement le format de compression
|
||||||
|
/// grâce à `niffler::sniff` ou via l'extension.
|
||||||
|
pub fn open(path: &Path) -> io::Result<Self> {
|
||||||
|
let file = File::open(path)?;
|
||||||
|
// `niffler::sniff` examine les premiers octets pour choisir le décompresseur
|
||||||
|
let reader = match niffler::sniff(Box::new(file)) {
|
||||||
|
Ok(r) => r,
|
||||||
|
Err(e) => {
|
||||||
|
// Si aucune signature connue, on suppose raw
|
||||||
|
eprintln!("Aucune signature de compression trouvée, lecture brute.");
|
||||||
|
Box::new(BufReader::new(file)) as Box<dyn Read + Send>
|
||||||
|
}
|
||||||
|
};
|
||||||
|
Ok(PartitionReader {
|
||||||
|
reader,
|
||||||
|
seq_buf: Vec::with_capacity(256),
|
||||||
|
})
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Lit le prochain super‑kmer. Retourne `None` à la fin du fichier.
|
||||||
|
pub fn read_next(&mut self) -> io::Result<Option<SuperKmer>> {
|
||||||
|
SuperKmer::read_raw(&mut self.reader, &mut self.seq_buf)
|
||||||
|
}
|
||||||
|
}
|
||||||
@@ -265,6 +265,20 @@ impl SuperKmer {
|
|||||||
buf
|
buf
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/// Returns the raw 32-bit header word for binary serialisation.
|
||||||
|
/// Bits [7:0] = seql encoding (0→256, 1-255 direct). Bits [31:8] = payload.
|
||||||
|
#[inline]
|
||||||
|
pub fn header_bits(&self) -> u32 {
|
||||||
|
self.header.0
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Returns a read-only view of the packed 2-bit sequence bytes.
|
||||||
|
/// Length is always `(seql() + 3) / 4` bytes.
|
||||||
|
#[inline]
|
||||||
|
pub fn seq_bytes(&self) -> &[u8] {
|
||||||
|
&self.seq
|
||||||
|
}
|
||||||
|
|
||||||
/// Extract the kmer of length k starting at nucleotide position i (0-based).
|
/// Extract the kmer of length k starting at nucleotide position i (0-based).
|
||||||
///
|
///
|
||||||
/// Returns an error if k is invalid (0 or > 32) or if position i + k exceeds the sequence length.
|
/// Returns an error if k is invalid (0 or > 32) or if position i + k exceeds the sequence length.
|
||||||
|
|||||||
@@ -0,0 +1,14 @@
|
|||||||
|
[package]
|
||||||
|
name = "obiskio"
|
||||||
|
version = "0.1.0"
|
||||||
|
edition = "2024"
|
||||||
|
|
||||||
|
[dependencies]
|
||||||
|
niffler = "3.0.0"
|
||||||
|
rustix = { version = "1.1.4", features = ["process"] }
|
||||||
|
lru = "0.12"
|
||||||
|
|
||||||
|
obikseq = { path = "../obikseq" }
|
||||||
|
|
||||||
|
[dev-dependencies]
|
||||||
|
tempfile = "3"
|
||||||
@@ -0,0 +1,94 @@
|
|||||||
|
use obikseq::superkmer::SuperKmer;
|
||||||
|
use std::io::{self, Read, Write};
|
||||||
|
|
||||||
|
/// Serialise one SuperKmer into `w` (uncompressed; caller must wrap with a compressor).
|
||||||
|
#[inline]
|
||||||
|
pub(crate) fn write_superkmer<W: Write>(w: &mut W, sk: &SuperKmer) -> io::Result<()> {
|
||||||
|
w.write_all(&sk.header_bits().to_le_bytes())?;
|
||||||
|
w.write_all(sk.seq_bytes())
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Deserialise one SuperKmer from `r`. Returns `None` on clean EOF.
|
||||||
|
/// `seq_buf` is a reusable scratch buffer to avoid per-record allocation.
|
||||||
|
pub(crate) fn read_superkmer<R: Read>(
|
||||||
|
r: &mut R,
|
||||||
|
seq_buf: &mut Vec<u8>,
|
||||||
|
) -> io::Result<Option<SuperKmer>> {
|
||||||
|
let mut hdr = [0u8; 4];
|
||||||
|
match r.read_exact(&mut hdr) {
|
||||||
|
Ok(()) => {}
|
||||||
|
Err(e) if e.kind() == io::ErrorKind::UnexpectedEof => return Ok(None),
|
||||||
|
Err(e) => return Err(e),
|
||||||
|
}
|
||||||
|
let bits = u32::from_le_bytes(hdr);
|
||||||
|
let seql_byte = (bits & 0xFF) as u8;
|
||||||
|
let nt_len: usize = if seql_byte == 0 { 256 } else { seql_byte as usize };
|
||||||
|
let byte_len = (nt_len + 3) / 4;
|
||||||
|
seq_buf.resize(byte_len, 0);
|
||||||
|
r.read_exact(seq_buf)?;
|
||||||
|
Ok(Some(SuperKmer::new(seql_byte, seq_buf.as_slice().into())))
|
||||||
|
}
|
||||||
|
|
||||||
|
#[cfg(test)]
|
||||||
|
mod tests {
|
||||||
|
use super::*;
|
||||||
|
use std::io::Cursor;
|
||||||
|
|
||||||
|
fn make_sk(ascii: &[u8]) -> SuperKmer {
|
||||||
|
SuperKmer::from_ascii(ascii)
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn roundtrip_single() {
|
||||||
|
let sk = make_sk(b"ACGTACGT");
|
||||||
|
let mut buf = Vec::new();
|
||||||
|
write_superkmer(&mut buf, &sk).unwrap();
|
||||||
|
|
||||||
|
let mut cur = Cursor::new(&buf);
|
||||||
|
let mut seq_buf = Vec::new();
|
||||||
|
let got = read_superkmer(&mut cur, &mut seq_buf).unwrap().unwrap();
|
||||||
|
assert_eq!(sk.to_ascii(), got.to_ascii());
|
||||||
|
assert_eq!(sk.seql(), got.seql());
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn roundtrip_all_lengths() {
|
||||||
|
let bases: Vec<u8> = (0..256).map(|i| b"ACGT"[i % 4]).collect();
|
||||||
|
for len in (1..=9).chain([255, 256]) {
|
||||||
|
let sk = make_sk(&bases[..len]);
|
||||||
|
let mut buf = Vec::new();
|
||||||
|
write_superkmer(&mut buf, &sk).unwrap();
|
||||||
|
|
||||||
|
let mut cur = Cursor::new(&buf);
|
||||||
|
let mut seq_buf = Vec::new();
|
||||||
|
let got = read_superkmer(&mut cur, &mut seq_buf).unwrap().unwrap();
|
||||||
|
assert_eq!(sk.to_ascii(), got.to_ascii(), "len={len}");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn eof_returns_none() {
|
||||||
|
let buf: Vec<u8> = vec![];
|
||||||
|
let mut cur = Cursor::new(&buf);
|
||||||
|
let mut seq_buf = Vec::new();
|
||||||
|
assert!(read_superkmer(&mut cur, &mut seq_buf).unwrap().is_none());
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn multiple_records() {
|
||||||
|
let seqs: &[&[u8]] = &[b"AAAA", b"CCCC", b"GGGG", b"TTTT"];
|
||||||
|
let mut buf = Vec::new();
|
||||||
|
for s in seqs {
|
||||||
|
write_superkmer(&mut buf, &make_sk(s)).unwrap();
|
||||||
|
}
|
||||||
|
|
||||||
|
let mut cur = Cursor::new(&buf);
|
||||||
|
let mut seq_buf = Vec::new();
|
||||||
|
for s in seqs {
|
||||||
|
let got = read_superkmer(&mut cur, &mut seq_buf).unwrap().unwrap();
|
||||||
|
let expected = make_sk(s);
|
||||||
|
assert_eq!(expected.to_ascii(), got.to_ascii());
|
||||||
|
}
|
||||||
|
assert!(read_superkmer(&mut cur, &mut seq_buf).unwrap().is_none());
|
||||||
|
}
|
||||||
|
}
|
||||||
@@ -0,0 +1,40 @@
|
|||||||
|
use std::fmt;
|
||||||
|
use std::io;
|
||||||
|
|
||||||
|
#[derive(Debug)]
|
||||||
|
pub enum SKError {
|
||||||
|
Io(io::Error),
|
||||||
|
Compression(niffler::Error),
|
||||||
|
}
|
||||||
|
|
||||||
|
pub type SKResult<T> = Result<T, SKError>;
|
||||||
|
|
||||||
|
impl fmt::Display for SKError {
|
||||||
|
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
|
||||||
|
match self {
|
||||||
|
SKError::Io(e) => write!(f, "I/O error: {e}"),
|
||||||
|
SKError::Compression(e) => write!(f, "compression error: {e}"),
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
impl std::error::Error for SKError {
|
||||||
|
fn source(&self) -> Option<&(dyn std::error::Error + 'static)> {
|
||||||
|
match self {
|
||||||
|
SKError::Io(e) => Some(e),
|
||||||
|
SKError::Compression(e) => Some(e),
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
impl From<io::Error> for SKError {
|
||||||
|
fn from(e: io::Error) -> Self {
|
||||||
|
SKError::Io(e)
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
impl From<niffler::Error> for SKError {
|
||||||
|
fn from(e: niffler::Error) -> Self {
|
||||||
|
SKError::Compression(e)
|
||||||
|
}
|
||||||
|
}
|
||||||
@@ -0,0 +1,9 @@
|
|||||||
|
pub mod codec;
|
||||||
|
pub mod error;
|
||||||
|
pub mod limits;
|
||||||
|
pub mod pool;
|
||||||
|
pub mod reader;
|
||||||
|
|
||||||
|
pub use error::{SKError, SKResult};
|
||||||
|
pub use pool::{create_token, create_token_with, SKFilePool, SharedPool, SKFileWriter};
|
||||||
|
pub use reader::{SKFileIter, SKFileReader};
|
||||||
@@ -0,0 +1,8 @@
|
|||||||
|
use rustix::process::{Resource, getrlimit};
|
||||||
|
|
||||||
|
/// Returns the maximum number of file descriptors that can be simultaneously open
|
||||||
|
/// for the current process. This is the process' file descriptor limit as
|
||||||
|
/// configured by the operating system.
|
||||||
|
pub fn max_concurrent_files() -> Option<u64> {
|
||||||
|
getrlimit(Resource::Nofile).current
|
||||||
|
}
|
||||||
@@ -0,0 +1,615 @@
|
|||||||
|
use crate::codec::write_superkmer;
|
||||||
|
use crate::error::SKResult;
|
||||||
|
use crate::limits::max_concurrent_files;
|
||||||
|
use lru::LruCache;
|
||||||
|
use niffler::send::compression::Format;
|
||||||
|
use niffler::Level;
|
||||||
|
use obikseq::superkmer::SuperKmer;
|
||||||
|
use std::fs::{File, OpenOptions};
|
||||||
|
use std::io::{BufWriter, Write};
|
||||||
|
use std::num::NonZeroUsize;
|
||||||
|
use std::path::{Path, PathBuf};
|
||||||
|
use std::sync::{Arc, Mutex, OnceLock};
|
||||||
|
|
||||||
|
/// Hard upper bound on pool size regardless of OS fd limit.
|
||||||
|
pub const MAX_POOL_SIZE: usize = 512;
|
||||||
|
|
||||||
|
/// Default pending buffer threshold (bytes) before draining to the physical fd.
|
||||||
|
pub const DEFAULT_FLUSH_THRESHOLD: usize = 8 * 1024;
|
||||||
|
|
||||||
|
// Convenient alias for the per-entry physical writer slot.
|
||||||
|
type PhysWriter = Option<Box<dyn Write + Send>>;
|
||||||
|
|
||||||
|
// ── WriteEntry ─────────────────────────────────────────────────────────────────
|
||||||
|
|
||||||
|
struct WriteEntry {
|
||||||
|
path: PathBuf,
|
||||||
|
format: Format,
|
||||||
|
level: Level,
|
||||||
|
/// Per-entry mutex for the physical fd.
|
||||||
|
/// Independent of the pool mutex to allow parallel writes to different entries.
|
||||||
|
fd: Arc<Mutex<PhysWriter>>,
|
||||||
|
logically_closed: bool,
|
||||||
|
}
|
||||||
|
|
||||||
|
// ── SKFilePool ─────────────────────────────────────────────────────────────────
|
||||||
|
|
||||||
|
/// LRU pool of open write file descriptors.
|
||||||
|
///
|
||||||
|
/// # Locking model
|
||||||
|
///
|
||||||
|
/// Two independent locks:
|
||||||
|
///
|
||||||
|
/// | Lock | Scope | Held during |
|
||||||
|
/// |---|---|---|
|
||||||
|
/// | `Arc<Mutex<SKFilePool>>` (pool lock) | all entries | LRU management only — microseconds |
|
||||||
|
/// | `Arc<Mutex<PhysWriter>>` (entry lock) | one entry | Writing a pending buffer to the fd |
|
||||||
|
///
|
||||||
|
/// **Pool lock is never held while writing data.** This allows parallel writes
|
||||||
|
/// to different partitions.
|
||||||
|
///
|
||||||
|
/// Lock ordering: always pool lock → entry lock, never reverse.
|
||||||
|
///
|
||||||
|
/// # Eviction
|
||||||
|
///
|
||||||
|
/// `evict_lru()` uses `try_lock()` on entry fd locks.
|
||||||
|
/// An entry whose fd is currently being written to is skipped; the next LRU
|
||||||
|
/// candidate is tried instead. If all open fds are in use, an error is returned.
|
||||||
|
pub struct SKFilePool {
|
||||||
|
max_open: usize,
|
||||||
|
/// All registered entries. Index = stable token id. Never shrinks.
|
||||||
|
entries: Vec<WriteEntry>,
|
||||||
|
/// IDs of entries currently holding an open fd, in LRU order.
|
||||||
|
///
|
||||||
|
/// Invariant: `id ∈ open ↔ entries[id].fd.lock().is_some()`
|
||||||
|
open: LruCache<usize, ()>,
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Shared reference to a pool; the primary way to create `SKFileWriter`s.
|
||||||
|
pub type SharedPool = Arc<Mutex<SKFilePool>>;
|
||||||
|
|
||||||
|
static GLOBAL_POOL: OnceLock<SharedPool> = OnceLock::new();
|
||||||
|
|
||||||
|
fn global_pool() -> &'static SharedPool {
|
||||||
|
GLOBAL_POOL.get_or_init(|| Arc::new(Mutex::new(SKFilePool::from_system_limits())))
|
||||||
|
}
|
||||||
|
|
||||||
|
impl SKFilePool {
|
||||||
|
/// Create a pool allowing at most `max_open` simultaneously open fds.
|
||||||
|
pub fn new(max_open: usize) -> Self {
|
||||||
|
let cap = NonZeroUsize::new(max_open.max(1)).unwrap();
|
||||||
|
Self { max_open, entries: Vec::new(), open: LruCache::new(cap) }
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Derive pool size from the OS fd limit (75 %, clamped to `[16, MAX_POOL_SIZE]`).
|
||||||
|
pub fn from_system_limits() -> Self {
|
||||||
|
let fd_limit = max_concurrent_files().unwrap_or(256) as usize;
|
||||||
|
let max_open = (fd_limit * 3 / 4).clamp(16, MAX_POOL_SIZE);
|
||||||
|
Self::new(max_open)
|
||||||
|
}
|
||||||
|
|
||||||
|
pub fn max_open(&self) -> usize {
|
||||||
|
self.max_open
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Total number of registered entries (open + evicted).
|
||||||
|
pub fn len(&self) -> usize {
|
||||||
|
self.entries.len()
|
||||||
|
}
|
||||||
|
|
||||||
|
pub fn is_empty(&self) -> bool {
|
||||||
|
self.entries.is_empty()
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Number of currently open fds — O(1).
|
||||||
|
pub fn open_count(&self) -> usize {
|
||||||
|
self.open.len()
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Flush and close all registered entries. O(n), one-time.
|
||||||
|
///
|
||||||
|
/// Call only after all concurrent drains have completed (e.g., after joining
|
||||||
|
/// all write threads). Tokens with unflushed pending must be flushed or closed
|
||||||
|
/// before this call, or their data will be lost.
|
||||||
|
pub fn close_all(&mut self) -> SKResult<()> {
|
||||||
|
for entry in self.entries.iter_mut() {
|
||||||
|
entry.logically_closed = true;
|
||||||
|
let mut fd_guard = entry.fd.lock().unwrap();
|
||||||
|
if let Some(mut w) = fd_guard.take() {
|
||||||
|
w.flush()?;
|
||||||
|
// drop(w) → Zstd frame footer written
|
||||||
|
}
|
||||||
|
}
|
||||||
|
self.open.clear();
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
|
||||||
|
// ── private ───────────────────────────────────────────────────────────────
|
||||||
|
|
||||||
|
/// Create file on disk (empty Zstd frame, fd immediately closed), register entry.
|
||||||
|
fn register(&mut self, path: PathBuf, format: Format, level: Level) -> SKResult<usize> {
|
||||||
|
{
|
||||||
|
let file = File::create(&path)?;
|
||||||
|
let _w = niffler::send::get_writer(Box::new(BufWriter::new(file)), format, level)?;
|
||||||
|
// _w drops here → empty frame finalized, fd released
|
||||||
|
}
|
||||||
|
let id = self.entries.len();
|
||||||
|
self.entries.push(WriteEntry {
|
||||||
|
path,
|
||||||
|
format,
|
||||||
|
level,
|
||||||
|
fd: Arc::new(Mutex::new(None)),
|
||||||
|
logically_closed: false,
|
||||||
|
});
|
||||||
|
Ok(id)
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Ensure entry `id` has an open fd. Evicts LRU if at capacity.
|
||||||
|
/// Must be called under pool lock.
|
||||||
|
fn ensure_open(&mut self, id: usize) -> SKResult<()> {
|
||||||
|
if self.open.contains(&id) {
|
||||||
|
return Ok(());
|
||||||
|
}
|
||||||
|
if self.entries[id].logically_closed {
|
||||||
|
return Err(std::io::Error::new(
|
||||||
|
std::io::ErrorKind::BrokenPipe,
|
||||||
|
"write to logically closed entry",
|
||||||
|
)
|
||||||
|
.into());
|
||||||
|
}
|
||||||
|
if self.open.len() >= self.max_open {
|
||||||
|
self.evict_lru()?;
|
||||||
|
}
|
||||||
|
let entry = &self.entries[id];
|
||||||
|
let file = OpenOptions::new().append(true).open(&entry.path)?;
|
||||||
|
let writer =
|
||||||
|
niffler::send::get_writer(Box::new(BufWriter::new(file)), entry.format, entry.level)?;
|
||||||
|
// Brief fd lock acquisition under pool lock. fd is None here so uncontested.
|
||||||
|
*self.entries[id].fd.lock().unwrap() = Some(writer);
|
||||||
|
self.open.put(id, ());
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Evict the least recently used *non-busy* entry. O(1) typical; O(open) worst-case.
|
||||||
|
///
|
||||||
|
/// Uses `try_lock()` so that entries currently being written to are skipped.
|
||||||
|
/// Returns an error if all open fds are in use.
|
||||||
|
fn evict_lru(&mut self) -> SKResult<()> {
|
||||||
|
// iter() yields MRU→LRU; rev() gives LRU→MRU (try least recently used first).
|
||||||
|
let candidates: Vec<usize> = self.open.iter().rev().map(|(&id, _)| id).collect();
|
||||||
|
for lru_id in candidates {
|
||||||
|
let fd_arc = Arc::clone(&self.entries[lru_id].fd);
|
||||||
|
if let Ok(mut fd_guard) = fd_arc.try_lock() {
|
||||||
|
if let Some(mut w) = fd_guard.take() {
|
||||||
|
let _ = w.flush(); // best-effort; drop finalizes Zstd frame
|
||||||
|
}
|
||||||
|
self.open.pop(&lru_id);
|
||||||
|
return Ok(());
|
||||||
|
}
|
||||||
|
// fd locked by a writer thread — skip this candidate
|
||||||
|
}
|
||||||
|
Err(std::io::Error::new(
|
||||||
|
std::io::ErrorKind::ResourceBusy,
|
||||||
|
"pool saturated: all open fds are currently in use",
|
||||||
|
)
|
||||||
|
.into())
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// ── SKFileWriter ────────────────────────────────────────────────────────────────
|
||||||
|
|
||||||
|
/// Handle to a registered pool entry; owns a local pending write buffer.
|
||||||
|
///
|
||||||
|
/// # Write path (hot path)
|
||||||
|
///
|
||||||
|
/// `write(sk)` serialises into `pending` with **no locking**.
|
||||||
|
/// When `pending ≥ flush_threshold`, `drain()` is called:
|
||||||
|
///
|
||||||
|
/// 1. Pool lock acquired briefly → `ensure_open(id)` → entry fd lock acquired **under** pool lock.
|
||||||
|
/// 2. Pool lock released. Entry fd lock still held.
|
||||||
|
/// 3. Entire `pending` buffer written to fd in one `write_all`. Entry fd lock released.
|
||||||
|
///
|
||||||
|
/// Acquiring the fd lock while the pool lock is still held prevents a race where
|
||||||
|
/// another thread could evict the just-opened fd between releasing pool lock and
|
||||||
|
/// acquiring fd lock. `evict_lru()` uses `try_lock()` and will skip an entry
|
||||||
|
/// whose fd lock is already held.
|
||||||
|
pub struct SKFileWriter {
|
||||||
|
id: usize,
|
||||||
|
pool: Arc<Mutex<SKFilePool>>,
|
||||||
|
path: PathBuf,
|
||||||
|
pending: Vec<u8>,
|
||||||
|
flush_threshold: usize,
|
||||||
|
logically_closed: bool,
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Create a `SKFileWriter` for a new file (Zstd, level 3).
|
||||||
|
pub fn create_token(pool: &SharedPool, path: PathBuf) -> SKResult<SKFileWriter> {
|
||||||
|
create_token_with(pool, path, Format::Zstd, Level::Three)
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Create a `SKFileWriter` for a new file with explicit format and level.
|
||||||
|
pub fn create_token_with(
|
||||||
|
pool: &SharedPool,
|
||||||
|
path: PathBuf,
|
||||||
|
format: Format,
|
||||||
|
level: Level,
|
||||||
|
) -> SKResult<SKFileWriter> {
|
||||||
|
let id = pool.lock().unwrap().register(path.clone(), format, level)?;
|
||||||
|
Ok(SKFileWriter {
|
||||||
|
id,
|
||||||
|
pool: Arc::clone(pool),
|
||||||
|
path,
|
||||||
|
pending: Vec::with_capacity(DEFAULT_FLUSH_THRESHOLD + 128),
|
||||||
|
flush_threshold: DEFAULT_FLUSH_THRESHOLD,
|
||||||
|
logically_closed: false,
|
||||||
|
})
|
||||||
|
}
|
||||||
|
|
||||||
|
impl SKFileWriter {
|
||||||
|
/// Create a standalone file writer (Zstd, level 3).
|
||||||
|
/// The pool is created internally and is not accessible to the caller.
|
||||||
|
pub fn create<P: AsRef<Path>>(path: P) -> SKResult<Self> {
|
||||||
|
Self::create_with(path, Format::Zstd, Level::Three)
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Create a standalone file writer with explicit format and level.
|
||||||
|
pub fn create_with<P: AsRef<Path>>(path: P, format: Format, level: Level) -> SKResult<Self> {
|
||||||
|
create_token_with(global_pool(), path.as_ref().to_owned(), format, level)
|
||||||
|
}
|
||||||
|
|
||||||
|
/// `true` if the underlying fd is currently open in the pool.
|
||||||
|
pub fn is_physically_open(&self) -> bool {
|
||||||
|
self.pool.lock().unwrap().open.contains(&self.id)
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Accumulate one SuperKmer. Drains to fd when `pending ≥ flush_threshold`.
|
||||||
|
pub fn write(&mut self, sk: &SuperKmer) -> SKResult<()> {
|
||||||
|
self.check_not_closed()?;
|
||||||
|
write_superkmer(&mut self.pending, sk)?;
|
||||||
|
if self.pending.len() >= self.flush_threshold {
|
||||||
|
self.drain()?;
|
||||||
|
}
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Accumulate a slice of SuperKmers, draining whenever the threshold is exceeded.
|
||||||
|
pub fn write_batch(&mut self, sks: &[SuperKmer]) -> SKResult<()> {
|
||||||
|
self.check_not_closed()?;
|
||||||
|
for sk in sks {
|
||||||
|
write_superkmer(&mut self.pending, sk)?;
|
||||||
|
if self.pending.len() >= self.flush_threshold {
|
||||||
|
self.drain()?;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Drain pending bytes to the fd **and** flush the compressor's internal buffer.
|
||||||
|
pub fn flush(&mut self) -> SKResult<()> {
|
||||||
|
self.check_not_closed()?;
|
||||||
|
if self.pending.is_empty() {
|
||||||
|
return Ok(());
|
||||||
|
}
|
||||||
|
let fd_arc;
|
||||||
|
let mut fd_guard;
|
||||||
|
{
|
||||||
|
let mut pool = self.pool.lock().unwrap();
|
||||||
|
pool.ensure_open(self.id)?;
|
||||||
|
let _ = pool.open.get(&self.id);
|
||||||
|
fd_arc = Arc::clone(&pool.entries[self.id].fd);
|
||||||
|
fd_guard = fd_arc.lock().unwrap(); // acquire fd lock under pool lock
|
||||||
|
// pool drops here → pool lock released, fd lock still held
|
||||||
|
}
|
||||||
|
let w = fd_guard.as_mut().expect("fd open after ensure_open");
|
||||||
|
w.write_all(&self.pending)?;
|
||||||
|
w.flush()?;
|
||||||
|
self.pending.clear();
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Flush pending bytes, finalize Zstd frame, permanently seal this token.
|
||||||
|
pub fn close(&mut self) -> SKResult<()> {
|
||||||
|
if self.logically_closed {
|
||||||
|
return Ok(());
|
||||||
|
}
|
||||||
|
self.logically_closed = true;
|
||||||
|
|
||||||
|
let fd_arc;
|
||||||
|
let mut fd_guard;
|
||||||
|
{
|
||||||
|
let mut pool = self.pool.lock().unwrap();
|
||||||
|
let has_pending = !self.pending.is_empty();
|
||||||
|
if has_pending {
|
||||||
|
pool.ensure_open(self.id)?;
|
||||||
|
}
|
||||||
|
pool.entries[self.id].logically_closed = true;
|
||||||
|
pool.open.pop(&self.id);
|
||||||
|
fd_arc = Arc::clone(&pool.entries[self.id].fd);
|
||||||
|
fd_guard = fd_arc.lock().unwrap(); // acquire fd lock under pool lock
|
||||||
|
// pool drops here → pool lock released
|
||||||
|
}
|
||||||
|
|
||||||
|
if !self.pending.is_empty() {
|
||||||
|
fd_guard.as_mut().expect("fd open after ensure_open").write_all(&self.pending)?;
|
||||||
|
self.pending.clear();
|
||||||
|
}
|
||||||
|
if let Some(mut w) = fd_guard.take() {
|
||||||
|
w.flush()?;
|
||||||
|
// drop(w) → Zstd frame finalized
|
||||||
|
}
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Adjust the byte threshold at which pending is drained to the fd.
|
||||||
|
/// Default: `DEFAULT_FLUSH_THRESHOLD` (8 KiB).
|
||||||
|
pub fn set_flush_threshold(&mut self, bytes: usize) {
|
||||||
|
self.flush_threshold = bytes;
|
||||||
|
}
|
||||||
|
|
||||||
|
/// `true` if this token has not been closed.
|
||||||
|
pub fn is_open(&self) -> bool {
|
||||||
|
!self.logically_closed
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Physical path of the file.
|
||||||
|
pub fn path(&self) -> &Path {
|
||||||
|
&self.path
|
||||||
|
}
|
||||||
|
|
||||||
|
// ── private ───────────────────────────────────────────────────────────────
|
||||||
|
|
||||||
|
fn check_not_closed(&self) -> SKResult<()> {
|
||||||
|
if self.logically_closed {
|
||||||
|
Err(std::io::Error::new(
|
||||||
|
std::io::ErrorKind::BrokenPipe,
|
||||||
|
"write to logically closed SKFileWriter",
|
||||||
|
)
|
||||||
|
.into())
|
||||||
|
} else {
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Drain pending bytes to the fd (no compressor flush).
|
||||||
|
///
|
||||||
|
/// Two-phase locking:
|
||||||
|
/// 1. Pool lock → ensure_open → promote MRU → acquire entry fd lock (under pool lock).
|
||||||
|
/// 2. Release pool lock. Write pending under entry fd lock only.
|
||||||
|
///
|
||||||
|
/// Holding fd lock while releasing pool lock prevents eviction of our entry
|
||||||
|
/// during the write: `evict_lru` uses `try_lock` and will skip us.
|
||||||
|
fn drain(&mut self) -> SKResult<()> {
|
||||||
|
debug_assert!(!self.pending.is_empty());
|
||||||
|
let fd_arc;
|
||||||
|
let mut fd_guard;
|
||||||
|
{
|
||||||
|
let mut pool = self.pool.lock().unwrap();
|
||||||
|
pool.ensure_open(self.id)?;
|
||||||
|
let _ = pool.open.get(&self.id); // promote to MRU
|
||||||
|
fd_arc = Arc::clone(&pool.entries[self.id].fd);
|
||||||
|
fd_guard = fd_arc.lock().unwrap(); // acquire fd lock under pool lock
|
||||||
|
// pool drops here → pool lock released, fd lock still held
|
||||||
|
}
|
||||||
|
fd_guard.as_mut().expect("fd open after ensure_open").write_all(&self.pending)?;
|
||||||
|
// fd_guard drops → entry fd lock released
|
||||||
|
self.pending.clear();
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
impl Drop for SKFileWriter {
|
||||||
|
fn drop(&mut self) {
|
||||||
|
if !self.logically_closed {
|
||||||
|
let _ = self.close();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// ── tests ──────────────────────────────────────────────────────────────────────
|
||||||
|
|
||||||
|
#[cfg(test)]
|
||||||
|
mod tests {
|
||||||
|
use super::*;
|
||||||
|
use crate::reader::SKFileReader;
|
||||||
|
use obikseq::superkmer::SuperKmer;
|
||||||
|
use tempfile::{NamedTempFile, TempDir};
|
||||||
|
|
||||||
|
fn make_sk(seed: usize) -> SuperKmer {
|
||||||
|
let bases: Vec<u8> = (0..8).map(|j| b"ACGT"[(seed + j) % 4]).collect();
|
||||||
|
SuperKmer::from_ascii(&bases)
|
||||||
|
}
|
||||||
|
|
||||||
|
fn pool(max_open: usize) -> SharedPool {
|
||||||
|
Arc::new(Mutex::new(SKFilePool::new(max_open)))
|
||||||
|
}
|
||||||
|
|
||||||
|
fn open_token(t: &mut SKFileWriter, sk: &SuperKmer) {
|
||||||
|
t.set_flush_threshold(1);
|
||||||
|
t.write(sk).unwrap(); // pending ≥ 1 → drain → fd opened
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn creation_holds_no_fd() {
|
||||||
|
let dir = TempDir::new().unwrap();
|
||||||
|
let p = pool(3);
|
||||||
|
for i in 0..10 {
|
||||||
|
create_token(&p, dir.path().join(format!("p{i}.zst"))).unwrap();
|
||||||
|
}
|
||||||
|
assert_eq!(p.lock().unwrap().open_count(), 0);
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn pool_limits_open_fds() {
|
||||||
|
let dir = TempDir::new().unwrap();
|
||||||
|
let p = pool(3);
|
||||||
|
let sk = make_sk(0);
|
||||||
|
|
||||||
|
let mut tokens: Vec<SKFileWriter> = (0..6)
|
||||||
|
.map(|i| create_token(&p, dir.path().join(format!("p{i}.zst"))).unwrap())
|
||||||
|
.collect();
|
||||||
|
|
||||||
|
for t in tokens.iter_mut() {
|
||||||
|
open_token(t, &sk);
|
||||||
|
}
|
||||||
|
|
||||||
|
assert!(p.lock().unwrap().open_count() <= 3, "open={}", p.lock().unwrap().open_count());
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn evicted_token_stays_logically_open() {
|
||||||
|
let dir = TempDir::new().unwrap();
|
||||||
|
let p = pool(1);
|
||||||
|
let sk = make_sk(0);
|
||||||
|
|
||||||
|
let mut t0 = create_token(&p, dir.path().join("a.zst")).unwrap();
|
||||||
|
let mut t1 = create_token(&p, dir.path().join("b.zst")).unwrap();
|
||||||
|
|
||||||
|
open_token(&mut t0, &sk); // t0 fd open, pool full
|
||||||
|
open_token(&mut t1, &sk); // evicts t0, t1 fd open
|
||||||
|
|
||||||
|
assert!(t0.is_open(), "t0 must remain logically open after eviction");
|
||||||
|
assert_eq!(p.lock().unwrap().open_count(), 1);
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn evicted_data_readable_after_close_all() {
|
||||||
|
let dir = TempDir::new().unwrap();
|
||||||
|
let p = pool(1);
|
||||||
|
let sk = make_sk(0);
|
||||||
|
|
||||||
|
let mut t0 = create_token(&p, dir.path().join("a.zst")).unwrap();
|
||||||
|
let mut t1 = create_token(&p, dir.path().join("b.zst")).unwrap();
|
||||||
|
|
||||||
|
t0.set_flush_threshold(1);
|
||||||
|
t0.write(&sk).unwrap(); // t0 fd open, pool full
|
||||||
|
t1.set_flush_threshold(1);
|
||||||
|
t1.write(&sk).unwrap(); // evicts t0, t1 fd open
|
||||||
|
|
||||||
|
// t0 still has the record in pending (eviction just closed fd, pending stays in token)
|
||||||
|
// Actually: t0's pending was drained before drain() returned (drain clears pending).
|
||||||
|
// So t0 wrote its record, then was evicted (fd closed).
|
||||||
|
|
||||||
|
drop(t0);
|
||||||
|
drop(t1);
|
||||||
|
p.lock().unwrap().close_all().unwrap();
|
||||||
|
|
||||||
|
for name in &["a.zst", "b.zst"] {
|
||||||
|
let mut r = SKFileReader::open(dir.path().join(name)).unwrap();
|
||||||
|
let got = r.read_batch(10).unwrap();
|
||||||
|
assert_eq!(got.len(), 1, "{name}: expected 1 record");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn touch_moves_to_mru_so_lru_is_evicted() {
|
||||||
|
let dir = TempDir::new().unwrap();
|
||||||
|
let p = pool(2);
|
||||||
|
let sk = make_sk(0);
|
||||||
|
|
||||||
|
let mut t0 = create_token(&p, dir.path().join("a.zst")).unwrap();
|
||||||
|
let mut t1 = create_token(&p, dir.path().join("b.zst")).unwrap();
|
||||||
|
let mut t2 = create_token(&p, dir.path().join("c.zst")).unwrap();
|
||||||
|
|
||||||
|
open_token(&mut t0, &sk); // t0 open
|
||||||
|
open_token(&mut t1, &sk); // t1 open, t0 LRU
|
||||||
|
|
||||||
|
// Write to t0 again → t0 becomes MRU, t1 becomes LRU
|
||||||
|
t0.set_flush_threshold(1);
|
||||||
|
t0.write(&sk).unwrap();
|
||||||
|
|
||||||
|
// Writing to t2 fills pool (cap=2) → evicts LRU = t1
|
||||||
|
open_token(&mut t2, &sk);
|
||||||
|
|
||||||
|
let open_count = p.lock().unwrap().open_count();
|
||||||
|
assert!(open_count <= 2, "open_count={open_count}");
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn close_all_produces_readable_files() {
|
||||||
|
let dir = TempDir::new().unwrap();
|
||||||
|
let p = pool(8);
|
||||||
|
let paths: Vec<_> = (0..4).map(|i| dir.path().join(format!("{i}.zst"))).collect();
|
||||||
|
|
||||||
|
let mut tokens: Vec<SKFileWriter> =
|
||||||
|
paths.iter().map(|path| create_token(&p, path.clone()).unwrap()).collect();
|
||||||
|
|
||||||
|
for (i, t) in tokens.iter_mut().enumerate() {
|
||||||
|
t.write(&make_sk(i)).unwrap();
|
||||||
|
}
|
||||||
|
// close tokens first so pending bytes are flushed and Zstd frames finalized
|
||||||
|
for t in tokens.iter_mut() {
|
||||||
|
t.close().unwrap();
|
||||||
|
}
|
||||||
|
p.lock().unwrap().close_all().unwrap();
|
||||||
|
|
||||||
|
for path in &paths {
|
||||||
|
let mut r = SKFileReader::open(path).unwrap();
|
||||||
|
let got = r.read_batch(10).unwrap();
|
||||||
|
assert_eq!(got.len(), 1);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn write_batch_roundtrip() {
|
||||||
|
let dir = TempDir::new().unwrap();
|
||||||
|
let p = pool(4);
|
||||||
|
let sks: Vec<_> = (0..50).map(make_sk).collect();
|
||||||
|
let path = dir.path().join("batch.zst");
|
||||||
|
|
||||||
|
let mut t = create_token(&p, path.clone()).unwrap();
|
||||||
|
t.write_batch(&sks).unwrap();
|
||||||
|
t.close().unwrap();
|
||||||
|
|
||||||
|
let mut r = SKFileReader::open(&path).unwrap();
|
||||||
|
let got = r.read_batch(100).unwrap();
|
||||||
|
assert_eq!(got.len(), 50);
|
||||||
|
for (a, b) in sks.iter().zip(got.iter()) {
|
||||||
|
assert_eq!(a.to_ascii(), b.to_ascii());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn from_system_limits_bounded() {
|
||||||
|
let pool = SKFilePool::from_system_limits();
|
||||||
|
assert!(pool.max_open() >= 16);
|
||||||
|
assert!(pool.max_open() <= MAX_POOL_SIZE);
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn standalone_roundtrip_zstd() {
|
||||||
|
let tmp = NamedTempFile::new().unwrap();
|
||||||
|
let sks: Vec<_> = (0..100).map(make_sk).collect();
|
||||||
|
{
|
||||||
|
let mut w = SKFileWriter::create(tmp.path()).unwrap();
|
||||||
|
w.write_batch(&sks).unwrap();
|
||||||
|
w.close().unwrap();
|
||||||
|
}
|
||||||
|
let mut r = SKFileReader::open(tmp.path()).unwrap();
|
||||||
|
let got = r.read_batch(200).unwrap();
|
||||||
|
assert_eq!(got.len(), 100);
|
||||||
|
for (a, b) in sks.iter().zip(got.iter()) {
|
||||||
|
assert_eq!(a.to_ascii(), b.to_ascii());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn standalone_close_prevents_write() {
|
||||||
|
let tmp = NamedTempFile::new().unwrap();
|
||||||
|
let mut w = SKFileWriter::create(tmp.path()).unwrap();
|
||||||
|
w.close().unwrap();
|
||||||
|
assert!(!w.is_open());
|
||||||
|
assert!(w.write(&make_sk(0)).is_err());
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn standalone_is_physically_open() {
|
||||||
|
let tmp = NamedTempFile::new().unwrap();
|
||||||
|
let mut w = SKFileWriter::create(tmp.path()).unwrap();
|
||||||
|
assert!(!w.is_physically_open()); // fd deferred until first drain
|
||||||
|
w.set_flush_threshold(1);
|
||||||
|
w.write(&make_sk(0)).unwrap(); // triggers drain → fd opened
|
||||||
|
assert!(w.is_physically_open());
|
||||||
|
w.close().unwrap();
|
||||||
|
assert!(!w.is_physically_open());
|
||||||
|
}
|
||||||
|
}
|
||||||
@@ -0,0 +1,203 @@
|
|||||||
|
use crate::codec::read_superkmer;
|
||||||
|
use crate::error::{SKError, SKResult};
|
||||||
|
use obikseq::superkmer::SuperKmer;
|
||||||
|
use std::fs::File;
|
||||||
|
use std::io::BufReader;
|
||||||
|
use std::path::{Path, PathBuf};
|
||||||
|
|
||||||
|
/// Binary reader for SuperKmers, with transparent decompression via niffler.
|
||||||
|
///
|
||||||
|
/// Access is strictly sequential. Call [`iter`](SKFileReader::iter) to get an
|
||||||
|
/// [`Iterator`] over the SuperKmers.
|
||||||
|
///
|
||||||
|
/// The reader also supports LRU-pool eviction and recovery: when physically
|
||||||
|
/// closed by the pool, it records how many SuperKmers have been consumed so
|
||||||
|
/// that it can fast-forward on next open.
|
||||||
|
pub struct SKFileReader {
|
||||||
|
path: PathBuf,
|
||||||
|
reader: Option<Box<dyn std::io::Read + Send>>,
|
||||||
|
/// Reusable scratch buffer for the `seq` bytes of each record.
|
||||||
|
seq_buf: Vec<u8>,
|
||||||
|
/// Number of SuperKmers successfully read so far (for eviction recovery).
|
||||||
|
consumed: u64,
|
||||||
|
}
|
||||||
|
|
||||||
|
impl SKFileReader {
|
||||||
|
/// Open a file for reading. Format is auto-detected from magic bytes.
|
||||||
|
pub fn open<P: AsRef<Path>>(path: P) -> SKResult<Self> {
|
||||||
|
let path = path.as_ref().to_owned();
|
||||||
|
let (reader, _fmt) = niffler::send::get_reader(Box::new(BufReader::new(File::open(&path)?)))?;
|
||||||
|
Ok(Self {
|
||||||
|
path,
|
||||||
|
reader: Some(reader),
|
||||||
|
seq_buf: Vec::with_capacity(64),
|
||||||
|
consumed: 0,
|
||||||
|
})
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Read the next SuperKmer, or `None` at EOF.
|
||||||
|
pub fn read(&mut self) -> SKResult<Option<SuperKmer>> {
|
||||||
|
let r = self.reader.as_mut().ok_or_else(|| {
|
||||||
|
std::io::Error::new(
|
||||||
|
std::io::ErrorKind::BrokenPipe,
|
||||||
|
"read from physically closed SKFileReader",
|
||||||
|
)
|
||||||
|
})?;
|
||||||
|
let result = read_superkmer(r, &mut self.seq_buf)?;
|
||||||
|
if result.is_some() {
|
||||||
|
self.consumed += 1;
|
||||||
|
}
|
||||||
|
Ok(result)
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Read up to `n` SuperKmers.
|
||||||
|
pub fn read_batch(&mut self, n: usize) -> SKResult<Vec<SuperKmer>> {
|
||||||
|
let mut batch = Vec::with_capacity(n);
|
||||||
|
for _ in 0..n {
|
||||||
|
match self.read()? {
|
||||||
|
Some(sk) => batch.push(sk),
|
||||||
|
None => break,
|
||||||
|
}
|
||||||
|
}
|
||||||
|
Ok(batch)
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Close the physical file handle without resetting the consumed counter.
|
||||||
|
pub fn close(&mut self) {
|
||||||
|
self.reader = None;
|
||||||
|
}
|
||||||
|
|
||||||
|
/// `true` if the underlying file handle is currently open.
|
||||||
|
pub fn is_open(&self) -> bool {
|
||||||
|
self.reader.is_some()
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Number of SuperKmers successfully read since the file was opened.
|
||||||
|
pub fn consumed(&self) -> u64 {
|
||||||
|
self.consumed
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Physical path of this file.
|
||||||
|
pub fn path(&self) -> &Path {
|
||||||
|
&self.path
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Return an iterator over this reader.
|
||||||
|
pub fn iter(&mut self) -> SKFileIter<'_> {
|
||||||
|
SKFileIter { reader: self, error: None }
|
||||||
|
}
|
||||||
|
|
||||||
|
// ── pool-internal helpers ─────────────────────────────────────────────────
|
||||||
|
|
||||||
|
/// Reopen after eviction and fast-forward to the last recorded position.
|
||||||
|
/// Cost is O(`consumed`) decompression; acceptable for sequential pipelines
|
||||||
|
/// where eviction of read-mode files is rare.
|
||||||
|
pub fn reopen_and_seek(&mut self) -> SKResult<()> {
|
||||||
|
debug_assert!(self.reader.is_none(), "reopen_and_seek on open reader");
|
||||||
|
let (reader, _fmt) =
|
||||||
|
niffler::send::get_reader(Box::new(BufReader::new(File::open(&self.path)?)))?;
|
||||||
|
self.reader = Some(reader);
|
||||||
|
let target = self.consumed;
|
||||||
|
self.consumed = 0;
|
||||||
|
for _ in 0..target {
|
||||||
|
match read_superkmer(self.reader.as_mut().unwrap(), &mut self.seq_buf)? {
|
||||||
|
Some(_) => self.consumed += 1,
|
||||||
|
None => break,
|
||||||
|
}
|
||||||
|
}
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// ── Iterator ─────────────────────────────────────────────────────────────────
|
||||||
|
|
||||||
|
/// Iterator adapter for [`SKFileReader`].
|
||||||
|
///
|
||||||
|
/// Errors during iteration are stored and accessible via [`take_error`](SKFileIter::take_error).
|
||||||
|
pub struct SKFileIter<'a> {
|
||||||
|
reader: &'a mut SKFileReader,
|
||||||
|
error: Option<SKError>,
|
||||||
|
}
|
||||||
|
|
||||||
|
impl<'a> SKFileIter<'a> {
|
||||||
|
/// Returns the first I/O error encountered during iteration, if any.
|
||||||
|
pub fn take_error(&mut self) -> Option<SKError> {
|
||||||
|
self.error.take()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
impl Iterator for SKFileIter<'_> {
|
||||||
|
type Item = SuperKmer;
|
||||||
|
|
||||||
|
fn next(&mut self) -> Option<SuperKmer> {
|
||||||
|
match self.reader.read() {
|
||||||
|
Ok(Some(sk)) => Some(sk),
|
||||||
|
Ok(None) => None,
|
||||||
|
Err(e) => {
|
||||||
|
self.error = Some(e);
|
||||||
|
None
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#[cfg(test)]
|
||||||
|
mod tests {
|
||||||
|
use super::*;
|
||||||
|
use crate::pool::SKFileWriter;
|
||||||
|
use tempfile::NamedTempFile;
|
||||||
|
|
||||||
|
fn make_sks(n: usize) -> Vec<SuperKmer> {
|
||||||
|
(0..n)
|
||||||
|
.map(|i| {
|
||||||
|
let bases: Vec<u8> = (0..8).map(|j| b"ACGT"[(i + j) % 4]).collect();
|
||||||
|
SuperKmer::from_ascii(&bases)
|
||||||
|
})
|
||||||
|
.collect()
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn iter_all() {
|
||||||
|
let tmp = NamedTempFile::new().unwrap();
|
||||||
|
let sks = make_sks(50);
|
||||||
|
|
||||||
|
{
|
||||||
|
let mut w = SKFileWriter::create(tmp.path()).unwrap();
|
||||||
|
w.write_batch(&sks).unwrap();
|
||||||
|
}
|
||||||
|
|
||||||
|
let mut r = SKFileReader::open(tmp.path()).unwrap();
|
||||||
|
let got: Vec<_> = r.iter().collect();
|
||||||
|
assert_eq!(got.len(), 50);
|
||||||
|
for (a, b) in sks.iter().zip(got.iter()) {
|
||||||
|
assert_eq!(a.to_ascii(), b.to_ascii());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#[test]
|
||||||
|
fn reopen_and_seek() {
|
||||||
|
let tmp = NamedTempFile::new().unwrap();
|
||||||
|
let sks = make_sks(20);
|
||||||
|
|
||||||
|
{
|
||||||
|
let mut w = SKFileWriter::create(tmp.path()).unwrap();
|
||||||
|
w.write_batch(&sks).unwrap();
|
||||||
|
}
|
||||||
|
|
||||||
|
let mut r = SKFileReader::open(tmp.path()).unwrap();
|
||||||
|
// Read 10, then simulate pool eviction + re-access
|
||||||
|
let first = r.read_batch(10).unwrap();
|
||||||
|
r.close();
|
||||||
|
r.reopen_and_seek().unwrap();
|
||||||
|
// Continue from position 10
|
||||||
|
let rest = r.read_batch(20).unwrap();
|
||||||
|
assert_eq!(first.len(), 10);
|
||||||
|
assert_eq!(rest.len(), 10);
|
||||||
|
for (a, b) in sks[..10].iter().zip(first.iter()) {
|
||||||
|
assert_eq!(a.to_ascii(), b.to_ascii());
|
||||||
|
}
|
||||||
|
for (a, b) in sks[10..].iter().zip(rest.iter()) {
|
||||||
|
assert_eq!(a.to_ascii(), b.to_ascii());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
Reference in New Issue
Block a user