majec-core 0.2.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- majec_core-0.2.0/.gitignore +1 -0
- majec_core-0.2.0/Cargo.lock +419 -0
- majec_core-0.2.0/Cargo.toml +19 -0
- majec_core-0.2.0/PKG-INFO +13 -0
- majec_core-0.2.0/pyproject.toml +24 -0
- majec_core-0.2.0/src/bam_processing.rs +1277 -0
- majec_core-0.2.0/src/exon_index.rs +272 -0
- majec_core-0.2.0/src/junction_metrics.rs +133 -0
- majec_core-0.2.0/src/lib.rs +20 -0
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286
|
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name = "pyo3"
|
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287
|
+
version = "0.29.3"
|
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288
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "700d18fa267b73b9b521fd7e13580e2f446916f176cacee1ab63fcc8191f1655"
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dependencies = [
|
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+
"libc",
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292
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"once_cell",
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293
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"portable-atomic",
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"pyo3-build-config",
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"pyo3-ffi",
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"pyo3-macros",
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]
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[[package]]
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name = "pyo3-build-config"
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301
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+
version = "0.29.3"
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302
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
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303
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checksum = "7b3fc0c4d08f6bb10e71fe39dfb9e2f59c6eb6854e22ec8092f50c69a4499adb"
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304
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+
dependencies = [
|
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305
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+
"target-lexicon",
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+
]
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+
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[[package]]
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309
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+
name = "pyo3-ffi"
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310
|
+
version = "0.29.3"
|
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311
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
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312
|
+
checksum = "dfc0b8e19df29aad7086cf977bb0c2a2f143e30567eb113e9cf72b62ca698330"
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+
dependencies = [
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314
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+
"libc",
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315
|
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"pyo3-build-config",
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+
]
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[[package]]
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name = "pyo3-macros"
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320
|
+
version = "0.29.3"
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321
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
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322
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+
checksum = "6100e8a4b5eba53afaa5ed078364851a0b2499c553a44c31026b929049b49dc6"
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323
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+
dependencies = [
|
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324
|
+
"proc-macro2",
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325
|
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"pyo3-macros-backend",
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"quote",
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"syn",
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]
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[[package]]
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331
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name = "pyo3-macros-backend"
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332
|
+
version = "0.29.3"
|
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333
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
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334
|
+
checksum = "6143877a16e82b5a727b7127ff4cd86858a24a28d745d72f43e6f227c7b1bdb3"
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335
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+
dependencies = [
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336
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+
"heck",
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337
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+
"proc-macro2",
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338
|
+
"quote",
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"syn",
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+
]
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+
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[[package]]
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|
+
name = "quote"
|
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344
|
+
version = "1.0.45"
|
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345
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
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346
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checksum = "41f2619966050689382d2b44f664f4bc593e129785a36d6ee376ddf37259b924"
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|
+
dependencies = [
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|
+
"proc-macro2",
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+
]
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|
+
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|
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[[package]]
|
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352
|
+
name = "rustc-hash"
|
|
353
|
+
version = "2.1.1"
|
|
354
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
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355
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checksum = "357703d41365b4b27c590e3ed91eabb1b663f07c4c084095e60cbed4362dff0d"
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|
+
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|
+
[[package]]
|
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358
|
+
name = "serde"
|
|
359
|
+
version = "1.0.228"
|
|
360
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
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|
361
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checksum = "9a8e94ea7f378bd32cbbd37198a4a91436180c5bb472411e48b5ec2e2124ae9e"
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362
|
+
dependencies = [
|
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363
|
+
"serde_core",
|
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364
|
+
]
|
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|
+
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|
+
[[package]]
|
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367
|
+
name = "serde_core"
|
|
368
|
+
version = "1.0.228"
|
|
369
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
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370
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checksum = "41d385c7d4ca58e59fc732af25c3983b67ac852c1a25000afe1175de458b67ad"
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371
|
+
dependencies = [
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|
372
|
+
"serde_derive",
|
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|
+
]
|
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|
+
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|
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[[package]]
|
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|
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name = "serde_derive"
|
|
377
|
+
version = "1.0.228"
|
|
378
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
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|
379
|
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checksum = "d540f220d3187173da220f885ab66608367b6574e925011a9353e4badda91d79"
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|
380
|
+
dependencies = [
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|
381
|
+
"proc-macro2",
|
|
382
|
+
"quote",
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383
|
+
"syn",
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384
|
+
]
|
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385
|
+
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|
+
[[package]]
|
|
387
|
+
name = "simd-adler32"
|
|
388
|
+
version = "0.3.9"
|
|
389
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
390
|
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checksum = "703d5c7ef118737c72f1af64ad2f6f8c5e1921f818cdcb97b8fe6fc69bf66214"
|
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391
|
+
|
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392
|
+
[[package]]
|
|
393
|
+
name = "syn"
|
|
394
|
+
version = "2.0.117"
|
|
395
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
396
|
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checksum = "e665b8803e7b1d2a727f4023456bbbbe74da67099c585258af0ad9c5013b9b99"
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|
397
|
+
dependencies = [
|
|
398
|
+
"proc-macro2",
|
|
399
|
+
"quote",
|
|
400
|
+
"unicode-ident",
|
|
401
|
+
]
|
|
402
|
+
|
|
403
|
+
[[package]]
|
|
404
|
+
name = "target-lexicon"
|
|
405
|
+
version = "0.13.5"
|
|
406
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
407
|
+
checksum = "adb6935a6f5c20170eeceb1a3835a49e12e19d792f6dd344ccc76a985ca5a6ca"
|
|
408
|
+
|
|
409
|
+
[[package]]
|
|
410
|
+
name = "unicode-ident"
|
|
411
|
+
version = "1.0.24"
|
|
412
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
413
|
+
checksum = "e6e4313cd5fcd3dad5cafa179702e2b244f760991f45397d14d4ebf38247da75"
|
|
414
|
+
|
|
415
|
+
[[package]]
|
|
416
|
+
name = "zlib-rs"
|
|
417
|
+
version = "0.6.3"
|
|
418
|
+
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
419
|
+
checksum = "3be3d40e40a133f9c916ee3f9f4fa2d9d63435b5fbe1bfc6d9dae0aa0ada1513"
|
|
@@ -0,0 +1,19 @@
|
|
|
1
|
+
[package]
|
|
2
|
+
name = "majec-core"
|
|
3
|
+
version = "0.2.0"
|
|
4
|
+
edition = "2021"
|
|
5
|
+
description = "High-performance EqC builder for MAJEC RNA-seq quantification"
|
|
6
|
+
|
|
7
|
+
[lib]
|
|
8
|
+
name = "majec_core"
|
|
9
|
+
crate-type = ["cdylib"]
|
|
10
|
+
|
|
11
|
+
[dependencies]
|
|
12
|
+
pyo3 = { version = "0.29", features = ["extension-module"] }
|
|
13
|
+
noodles = { version = "0.96", features = ["bam", "sam", "bgzf"] }
|
|
14
|
+
rustc-hash = "2" # Fast hashing for integer keys
|
|
15
|
+
|
|
16
|
+
[profile.release]
|
|
17
|
+
lto = true
|
|
18
|
+
codegen-units = 1
|
|
19
|
+
opt-level = 3
|
|
@@ -0,0 +1,13 @@
|
|
|
1
|
+
Metadata-Version: 2.4
|
|
2
|
+
Name: majec-core
|
|
3
|
+
Version: 0.2.0
|
|
4
|
+
Classifier: Programming Language :: Rust
|
|
5
|
+
Classifier: Programming Language :: Python :: 3.11
|
|
6
|
+
Classifier: Programming Language :: Python :: 3.12
|
|
7
|
+
Classifier: Programming Language :: Python :: 3.13
|
|
8
|
+
Classifier: License :: OSI Approved :: Apache Software License
|
|
9
|
+
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
|
|
10
|
+
Summary: Compiled (Rust) equivalence-class builder for MAJEC RNA-seq quantification
|
|
11
|
+
License: Apache-2.0
|
|
12
|
+
Requires-Python: >=3.11
|
|
13
|
+
Project-URL: Repository, https://github.com/calico/majec
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
[build-system]
|
|
2
|
+
requires = ["maturin>=1.0,<2.0"]
|
|
3
|
+
build-backend = "maturin"
|
|
4
|
+
|
|
5
|
+
[project]
|
|
6
|
+
name = "majec-core"
|
|
7
|
+
version = "0.2.0"
|
|
8
|
+
description = "Compiled (Rust) equivalence-class builder for MAJEC RNA-seq quantification"
|
|
9
|
+
requires-python = ">=3.11"
|
|
10
|
+
license = { text = "Apache-2.0" }
|
|
11
|
+
classifiers = [
|
|
12
|
+
"Programming Language :: Rust",
|
|
13
|
+
"Programming Language :: Python :: 3.11",
|
|
14
|
+
"Programming Language :: Python :: 3.12",
|
|
15
|
+
"Programming Language :: Python :: 3.13",
|
|
16
|
+
"License :: OSI Approved :: Apache Software License",
|
|
17
|
+
"Topic :: Scientific/Engineering :: Bio-Informatics",
|
|
18
|
+
]
|
|
19
|
+
|
|
20
|
+
[project.urls]
|
|
21
|
+
Repository = "https://github.com/calico/majec"
|
|
22
|
+
|
|
23
|
+
[tool.maturin]
|
|
24
|
+
features = ["pyo3/extension-module"]
|