OBIKmers/obikmer
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

+ obiskio: add binary I/O with LRU pool and compression

Browse Source 
- 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
2026-04-24 21:07:58 +02:00
parent d4e4289aff
commit c09d17401d
13 changed files with 1324 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files
src/Cargo.lock
Generated
+167 -4
View File
@@ -17,6 +17,12 @@ dependencies = [
"memchr",
]
[[package]]
name = "allocator-api2"
version = "0.2.21"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "683d7910e743518b0e34f1186f92494becacb047c7b6bf616c96772180fef923"
[[package]]
name = "anes"
version = "0.2.1"
@@ -85,6 +91,24 @@ version = "0.22.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6"
[[package]]
name = "bgzip"
version = "0.3.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "b64fd8980fb64af5951bc05de7772b598150a6f7eac42ec17f73e8489915f99b"
dependencies = [
"flate2",
"log",
"rayon",
"thiserror 1.0.69",
]
[[package]]
name = "bitflags"
version = "2.11.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "c4512299f36f043ab09a583e57bceb5a5aab7a73db1805848e8fef3c9e8c78b3"
[[package]]
name = "bitvec"
version = "1.0.1"
@@ -131,6 +155,15 @@ dependencies = [
"libc",
]
[[package]]
name = "bzip2"
version = "0.5.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "49ecfb22d906f800d4fe833b6282cf4dc1c298f5057ca0b5445e5c209735ca47"
dependencies = [
"bzip2-sys",
]
[[package]]
name = "bzip2-sys"
version = "0.1.13+1.0.8"
@@ -333,6 +366,28 @@ version = "1.15.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "48c757948c5ede0e46177b7add2e67155f70e33c07fea8284df6576da70b3719"
[[package]]
name = "equivalent"
version = "1.0.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "877a4ace8713b0bcf2a4e7eec82529c029f1d0619886d18145fea96c3ffe5c0f"
[[package]]
name = "errno"
version = "0.3.14"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "39cab71617ae0d63f51a36d69f866391735b51691dbda63cf6f96d042b63efeb"
dependencies = [
"libc",
"windows-sys 0.61.2",
]
[[package]]
name = "fastrand"
version = "2.4.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "9f1f227452a390804cdb637b74a86990f2a7d7ba4b7d5693aac9b4dd6defd8d6"
[[package]]
name = "find-msvc-tools"
version = "0.1.9"
@@ -355,6 +410,12 @@ version = "1.0.7"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1"
[[package]]
name = "foldhash"
version = "0.1.5"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "d9c4f5dac5e15c24eb999c26181a6ca40b39fe946cbe4c263c7209467bc83af2"
[[package]]
name = "form_urlencoded"
version = "1.2.2"
@@ -404,6 +465,17 @@ dependencies = [
"zerocopy",
]
[[package]]
name = "hashbrown"
version = "0.15.5"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "9229cfe53dfd69f0609a49f65461bd93001ea1ef889cd5529dd176593f5338a1"
dependencies = [
"allocator-api2",
"equivalent",
"foldhash",
]
[[package]]
name = "heck"
version = "0.5.0"
@@ -586,6 +658,12 @@ dependencies = [
"pkg-config",
]
[[package]]
name = "linux-raw-sys"
version = "0.12.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "32a66949e030da00e8c7d4434b251670a91556f4144941d37452769c25d58a53"
[[package]]
name = "litemap"
version = "0.8.2"
@@ -598,6 +676,15 @@ version = "0.4.29"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "5e5032e24019045c762d3c0f28f5b6b8bbf38563a65908389bf7978758920897"
[[package]]
name = "lru"
version = "0.12.5"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "234cf4f4a04dc1f57e24b96cc0cd600cf2af460d4161ac5ecdd0af8e1f3b2a38"
dependencies = [
"hashbrown",
]
[[package]]
name = "matchers"
version = "0.2.0"
@@ -629,11 +716,26 @@ version = "2.7.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "9e84f25af5326bacf3cbc3b9d2586d096426b10c889050cab891f89c9cb65932"
dependencies = [
"bzip2",
"bzip2 0.4.4",
"cfg-if",
"flate2",
"liblzma",
"thiserror",
"thiserror 2.0.18",
"zstd",
]
[[package]]
name = "niffler"
version = "3.0.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "62d3115cc93dac9fabdfd25f7d4fda51ad4a959fb4667d39af20f70bddfb3574"
dependencies = [
"bgzip",
"bzip2 0.5.2",
"cfg-if",
"flate2",
"liblzma",
"thiserror 2.0.18",
"zstd",
]
@@ -676,6 +778,10 @@ dependencies = [
"obiskbuilder",
]
[[package]]
name = "obikpartitionner"
version = "0.1.0"
[[package]]
name = "obikrope"
version = "0.1.0"
@@ -704,7 +810,7 @@ name = "obiread"
version = "0.1.0"
dependencies = [
"infer",
"niffler",
"niffler 2.7.0",
"obikrope",
"regex",
"tracing",
@@ -721,6 +827,17 @@ dependencies = [
"obikseq",
]
[[package]]
name = "obiskio"
version = "0.1.0"
dependencies = [
"lru",
"niffler 3.0.0",
"obikseq",
"rustix",
"tempfile",
]
[[package]]
name = "once_cell"
version = "1.21.4"
@@ -859,6 +976,19 @@ dependencies = [
"windows-sys 0.52.0",
]
[[package]]
name = "rustix"
version = "1.1.4"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "b6fe4565b9518b83ef4f91bb47ce29620ca828bd32cb7e408f0062e9930ba190"
dependencies = [
"bitflags",
"errno",
"libc",
"linux-raw-sys",
"windows-sys 0.61.2",
]
[[package]]
name = "rustls"
version = "0.23.38"
@@ -1025,13 +1155,46 @@ version = "1.0.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "55937e1799185b12863d447f42597ed69d9928686b8d88a1df17376a097d8369"
[[package]]
name = "tempfile"
version = "3.27.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "32497e9a4c7b38532efcdebeef879707aa9f794296a4f0244f6f69e9bc8574bd"
dependencies = [
"fastrand",
"getrandom 0.3.4",
"once_cell",
"rustix",
"windows-sys 0.61.2",
]
[[package]]
name = "thiserror"
version = "1.0.69"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "b6aaf5339b578ea85b50e080feb250a3e8ae8cfcdff9a461c9ec2904bc923f52"
dependencies = [
"thiserror-impl 1.0.69",
]
[[package]]
name = "thiserror"
version = "2.0.18"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "4288b5bcbc7920c07a1149a35cf9590a2aa808e0bc1eafaade0b80947865fbc4"
dependencies = [
"thiserror-impl",
"thiserror-impl 2.0.18",
]
[[package]]
name = "thiserror-impl"
version = "1.0.69"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "4fee6c4efc90059e10f81e6d42c60a18f76588c3d74cb83a0b242a2b6c7504c1"
dependencies = [
"proc-macro2",
"quote",
"syn",
]
[[package]]