PyPI - txnova - Versions diffs - 0.1.1__tar.gz - Mend

txnova 0.1.1__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.

Files changed (53) hide show

txnova-0.1.1/Cargo.lock +1042 -0
txnova-0.1.1/Cargo.toml +3 -0
txnova-0.1.1/LICENSE +202 -0
txnova-0.1.1/PKG-INFO +32 -0
txnova-0.1.1/README.md +53 -0
txnova-0.1.1/pyproject.toml +66 -0
txnova-0.1.1/python/txnova/__init__.py +7 -0
txnova-0.1.1/python/txnova/__main__.py +4 -0
txnova-0.1.1/python/txnova/assemble.py +131 -0
txnova-0.1.1/python/txnova/assembly_evidence.py +145 -0
txnova-0.1.1/python/txnova/cli.py +106 -0
txnova-0.1.1/python/txnova/config.py +133 -0
txnova-0.1.1/python/txnova/data/Mouse_Hexamer.tsv +4097 -0
txnova-0.1.1/python/txnova/data/SOURCE.txt +4 -0
txnova-0.1.1/python/txnova/errors.py +2 -0
txnova-0.1.1/python/txnova/fold.py +366 -0
txnova-0.1.1/python/txnova/function.py +184 -0
txnova-0.1.1/python/txnova/gates.py +596 -0
txnova-0.1.1/python/txnova/gene_score.py +422 -0
txnova-0.1.1/python/txnova/init_files.py +88 -0
txnova-0.1.1/python/txnova/leak.py +48 -0
txnova-0.1.1/python/txnova/logging.py +26 -0
txnova-0.1.1/python/txnova/naming.py +135 -0
txnova-0.1.1/python/txnova/orchestrator.py +822 -0
txnova-0.1.1/python/txnova/orphan.py +383 -0
txnova-0.1.1/python/txnova/preflight.py +67 -0
txnova-0.1.1/python/txnova/provenance.py +87 -0
txnova-0.1.1/python/txnova/report.py +636 -0
txnova-0.1.1/python/txnova/residual.py +651 -0
txnova-0.1.1/python/txnova/samples.py +91 -0
txnova-0.1.1/python/txnova/staging.py +82 -0
txnova-0.1.1/python/txnova/stamps.py +103 -0
txnova-0.1.1/python/txnova/stats.py +118 -0
txnova-0.1.1/python/txnova/templates/report.html.j2 +234 -0
txnova-0.1.1/rust/txnova-core/Cargo.toml +24 -0
txnova-0.1.1/rust/txnova-core/src/bam.rs +343 -0
txnova-0.1.1/rust/txnova-core/src/classcode.rs +325 -0
txnova-0.1.1/rust/txnova-core/src/coding.rs +271 -0
txnova-0.1.1/rust/txnova-core/src/coverage.rs +392 -0
txnova-0.1.1/rust/txnova-core/src/error.rs +19 -0
txnova-0.1.1/rust/txnova-core/src/fasta.rs +156 -0
txnova-0.1.1/rust/txnova-core/src/gtf.rs +400 -0
txnova-0.1.1/rust/txnova-core/src/interval.rs +109 -0
txnova-0.1.1/rust/txnova-core/src/leak.rs +512 -0
txnova-0.1.1/rust/txnova-core/src/lib.rs +173 -0
txnova-0.1.1/rust/txnova-core/src/orf.rs +224 -0
txnova-0.1.1/rust/txnova-core/src/preflight.rs +323 -0
txnova-0.1.1/rust/txnova-core/src/quantify.rs +379 -0
txnova-0.1.1/rust/txnova-core/src/splice.rs +77 -0
txnova-0.1.1/rust/txnova-core/src/structure.rs +436 -0
txnova-0.1.1/rust/txnova-core/src/sys_mem.rs +316 -0
txnova-0.1.1/rust/txnova-core/src/terminal.rs +313 -0
txnova-0.1.1/rust/txnova-core/src/types.rs +84 -0

txnova-0.1.1/Cargo.lock ADDED Viewed

@@ -0,0 +1,1042 @@
+# This file is automatically @generated by Cargo.
+# It is not intended for manual editing.
+version = 3
+[[package]]
+name = "aho-corasick"
+version = "1.1.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c982642fa9e8606056828ee9a8505737230110bb1099153c79efe865c59d12ba"
+dependencies = [
+ "memchr",
+]
+[[package]]
+name = "autocfg"
+version = "1.5.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f2032f911046de80f0a198e0901378627c33f59ea0ac00e363d481118bd70a53"
+[[package]]
+name = "bindgen"
+version = "0.72.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "993776b509cfb49c750f11b8f07a46fa23e0a1386ffc01fb1e7d343efc387895"
+dependencies = [
+ "bitflags",
+ "cexpr",
+ "clang-sys",
+ "itertools",
+ "proc-macro2",
+ "quote",
+ "regex",
+ "rustc-hash",
+ "shlex 1.3.0",
+ "syn 2.0.119",
+]
+[[package]]
+name = "bio-types"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f4dcf54f8b7f51450207d54780bab09c05f30b8b0caa991545082842e466ad7e"
+dependencies = [
+ "derive-new 0.6.0",
+ "lazy_static",
+ "regex",
+ "strum_macros",
+ "thiserror 1.0.69",
+]
+[[package]]
+name = "bitflags"
+version = "2.13.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b588b76d00fde79687d7646a9b5bdf3cc0f655e0bbd080335a95d7e96f3587da"
+[[package]]
+name = "block-buffer"
+version = "0.10.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71"
+dependencies = [
+ "generic-array",
+]
+[[package]]
+name = "byteorder"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b"
+[[package]]
+name = "cc"
+version = "1.4.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5d262e149917187838d5b42777c8253bcb64500067342904e7d429499a6f277e"
+dependencies = [
+ "find-msvc-tools",
+ "jobserver",
+ "libc",
+ "shlex 2.0.1",
+]
+[[package]]
+name = "cexpr"
+version = "0.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6fac387a98bb7c37292057cffc56d62ecb629900026402633ae9160df93a8766"
+dependencies = [
+ "nom",
+]
+[[package]]
+name = "cfg-if"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9330f8b2ff13f34540b44e946ef35111825727b38d33286ef986142615121801"
+[[package]]
+name = "clang-sys"
+version = "1.9.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "157a8ba7b480713b56f4c09fd13fc3e0a22a5dfab8097ba61cbc5feef950788a"
+dependencies = [
+ "glob",
+ "libc",
+ "libloading",
+]
+[[package]]
+name = "cmake"
+version = "0.1.58"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c0f78a02292a74a88ac736019ab962ece0bc380e3f977bf72e376c5d78ff0678"
+dependencies = [
+ "cc",
+]
+[[package]]
+name = "cpufeatures"
+version = "0.2.17"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "59ed5838eebb26a2bb2e58f6d5b5316989ae9d08bab10e0e6d103e656d1b0280"
+dependencies = [
+ "libc",
+]
+[[package]]
+name = "crypto-common"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "78c8292055d1c1df0cce5d180393dc8cce0abec0a7102adb6c7b1eef6016d60a"
+dependencies = [
+ "generic-array",
+ "typenum",
+]
+[[package]]
+name = "custom_derive"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9"
+[[package]]
+name = "derive-new"
+version = "0.5.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3418329ca0ad70234b9735dc4ceed10af4df60eff9c8e7b06cb5e520d92c3535"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 1.0.109",
+]
+[[package]]
+name = "derive-new"
+version = "0.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.119",
+]
+[[package]]
+name = "digest"
+version = "0.10.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9ed9a281f7bc9b7576e61468ba615a66a5c8cfdff42420a70aa82701a3b1e292"
+dependencies = [
+ "block-buffer",
+ "crypto-common",
+]
+[[package]]
+name = "displaydoc"
+version = "0.2.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c6232dd377dcc64799954cbd3a9bb882e9cdc1308ccd87b1c098f1fb2eaf82a8"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 3.0.3",
+]
+[[package]]
+name = "either"
+version = "1.17.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9e5e8f6c15a24b9a3ee5efec809ccd006d3b30e8b3bb63c39af737c7f87daa1d"
+[[package]]
+name = "find-msvc-tools"
+version = "0.1.10"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "26b73573e6edcd2af0cdf47bd6cb58f0b3839491263c314eaad1ccf24430e1de"
+[[package]]
+name = "form_urlencoded"
+version = "1.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cb4cb245038516f5f85277875cdaa4f7d2c9a0fa0468de06ed190163b1581fcf"
+dependencies = [
+ "percent-encoding",
+]
+[[package]]
+name = "fs-utils"
+version = "1.1.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6fc7a9dc005c944c98a935e7fd626faf5bf7e5a609f94bc13e42fc4a02e52593"
+dependencies = [
+ "quick-error",
+]
+[[package]]
+name = "generic-array"
+version = "0.14.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a"
+dependencies = [
+ "typenum",
+ "version_check",
+]
+[[package]]
+name = "getrandom"
+version = "0.4.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "300e883d756b2e4ec94e02791f39b04b522276138852cfc41d9fb7e904106099"
+dependencies = [
+ "cfg-if",
+ "libc",
+ "r-efi",
+]
+[[package]]
+name = "glob"
+version = "0.3.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e4eba85ea1d0a966a983acd07deee566e67395d2d96b6fb39e62b5a833f1eb0b"
+[[package]]
+name = "heck"
+version = "0.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
+[[package]]
+name = "hts-sys"
+version = "2.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fc7e68eb880b02c80cfb41e8dc7904062a3ea7e27b7c4556e88d648dd2f038da"
+dependencies = [
+ "bindgen",
+ "cc",
+ "fs-utils",
+ "glob",
+ "libz-sys",
+]
+[[package]]
+name = "icu_collections"
+version = "2.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fa68d21081c4a05d5a901a1c62add574c77048b6a1c67be3b50ce0b60d4ca513"
+dependencies = [
+ "displaydoc",
+ "potential_utf",
+ "utf8_iter",
+ "yoke",
+ "zerofrom",
+ "zerovec",
+]
+[[package]]
+name = "icu_locale_core"
+version = "2.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d56e28588da92eee5c3201a6eff33fabdd49b62269c8938d4ff050ce4d900deb"
+dependencies = [
+ "displaydoc",
+ "litemap",
+ "tinystr",
+ "writeable",
+ "zerovec",
+]
+[[package]]
+name = "icu_normalizer"
+version = "2.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "12f9cf5f235641ed274641dd81c3f28d870e276763d0797aeeab72317b1c646f"
+dependencies = [
+ "icu_collections",
+ "icu_normalizer_data",
+ "icu_properties",
+ "icu_provider",
+ "smallvec",
+ "zerovec",
+]
+[[package]]
+name = "icu_normalizer_data"
+version = "2.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1563da1ed3e0b3bf3d74c9b85917ac9c56464d2f57242270c09c9e752f8021a0"
+[[package]]
+name = "icu_properties"
+version = "2.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7e7ca276ad3145661a65914e6daf131ca5120cd3dcee8f8f3214b8875184a148"
+dependencies = [
+ "displaydoc",
+ "icu_collections",
+ "icu_locale_core",
+ "icu_properties_data",
+ "icu_provider",
+ "zerotrie",
+ "zerovec",
+]
+[[package]]
+name = "icu_properties_data"
+version = "2.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e590f038c1464a96894fd6d10127e90a8be4509f56ff7ecef851b15cee0b7caa"
+[[package]]
+name = "icu_provider"
+version = "2.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "92a7ed671a6aad807a8651a2e1782a6598fda9ce5185dd8158549e95a91c6428"
+dependencies = [
+ "displaydoc",
+ "icu_locale_core",
+ "writeable",
+ "yoke",
+ "zerofrom",
+ "zerotrie",
+ "zerovec",
+]
+[[package]]
+name = "idna"
+version = "1.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3b0875f23caa03898994f6ddc501886a45c7d3d62d04d2d90788d47be1b1e4de"
+dependencies = [
+ "idna_adapter",
+ "smallvec",
+ "utf8_iter",
+]
+[[package]]
+name = "idna_adapter"
+version = "1.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cb68373c0d6620ef8105e855e7745e18b0d00d3bdb07fb532e434244cdb9a714"
+dependencies = [
+ "icu_normalizer",
+ "icu_properties",
+]
+[[package]]
+name = "ieee754"
+version = "0.2.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9007da9cacbd3e6343da136e98b0d2df013f553d35bdec8b518f07bea768e19c"
+[[package]]
+name = "indoc"
+version = "2.0.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "79cf5c93f93228cf8efb3ba362535fb11199ac548a09ce117c9b1adc3030d706"
+dependencies = [
+ "rustversion",
+]
+[[package]]
+name = "itertools"
+version = "0.13.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "413ee7dfc52ee1a4949ceeb7dbc8a33f2d6c088194d9f922fb8318faf1f01186"
+dependencies = [
+ "either",
+]
+[[package]]
+name = "itoa"
+version = "1.0.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8f42a60cbdf9a97f5d2305f08a87dc4e09308d1276d28c869c684d7777685682"
+[[package]]
+name = "jobserver"
+version = "0.1.35"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1c00acbd29eabad4a2392fa0e921c874934dbbf4194312ad20f04a0ed67a3cb3"
+dependencies = [
+ "getrandom",
+ "libc",
+]
+[[package]]
+name = "lazy_static"
+version = "1.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
+[[package]]
+name = "libc"
+version = "0.2.189"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3eaf3ede3fee6db1a4c2ee091bf8a8b4dccdc6d17f656fb07896ee72867612f2"
+[[package]]
+name = "libloading"
+version = "0.8.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d7c4b02199fee7c5d21a5ae7d8cfa79a6ef5bb2fc834d6e9058e89c825efdc55"
+dependencies = [
+ "cfg-if",
+ "windows-link",
+]
+[[package]]
+name = "libz-sys"
+version = "1.1.29"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "85bc9657773828b90eeb625adff10eeac83cc21bbfd8e23a03eaa8a33c9e28d9"
+dependencies = [
+ "cc",
+ "cmake",
+ "libc",
+ "pkg-config",
+ "vcpkg",
+]
+[[package]]
+name = "linear-map"
+version = "1.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee"
+[[package]]
+name = "litemap"
+version = "0.8.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "47d9d19d1d6efa0109d2f65ff4c85cddd50bd572e5a00127ab10987290bcefae"
+[[package]]
+name = "memchr"
+version = "2.8.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cf8baf1c55e62ffcace7a9f06f4bd9cd3f0c4beb022d3b367256b91b87513d98"
+[[package]]
+name = "memoffset"
+version = "0.9.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "488016bfae457b036d996092f6cb448677611ce4449e970ceaf42695203f218a"
+dependencies = [
+ "autocfg",
+]
+[[package]]
+name = "minimal-lexical"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
+[[package]]
+name = "newtype_derive"
+version = "0.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ac8cd24d9f185bb7223958d8c1ff7a961b74b1953fd05dba7cc568a63b3861ec"
+dependencies = [
+ "rustc_version",
+]
+[[package]]
+name = "nom"
+version = "7.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d273983c5a657a70a3e8f2a01329822f3b8c8172b73826411a55751e404a0a4a"
+dependencies = [
+ "memchr",
+ "minimal-lexical",
+]
+[[package]]
+name = "once_cell"
+version = "1.21.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9f7c3e4beb33f85d45ae3e3a1792185706c8e16d043238c593331cc7cd313b50"
+[[package]]
+name = "percent-encoding"
+version = "2.3.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9b4f627cb1b25917193a259e49bdad08f671f8d9708acfd5fe0a8c1455d87220"
+[[package]]
+name = "pkg-config"
+version = "0.3.33"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "19f132c84eca552bf34cab8ec81f1c1dcc229b811638f9d283dceabe58c5569e"
+[[package]]
+name = "portable-atomic"
+version = "1.15.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "05c8b63e8d9609db387f0324918f81d68fe27748f084ef092fb35954d0539a85"
+[[package]]
+name = "potential_utf"
+version = "0.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d83eb9bc6d8e5cf568e7a1101d60ee05e81ed50ea106026f3d18deeb046d7661"
+dependencies = [
+ "zerovec",
+]
+[[package]]
+name = "proc-macro2"
+version = "1.0.107"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "985e7ec9bb745e6ce6535b544d84d6cd6f7ad8bd711c398938ae983b91a766d9"
+dependencies = [
+ "unicode-ident",
+]
+[[package]]
+name = "pyo3"
+version = "0.23.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7778bffd85cf38175ac1f545509665d0b9b92a198ca7941f131f85f7a4f9a872"
+dependencies = [
+ "cfg-if",
+ "indoc",
+ "libc",
+ "memoffset",
+ "once_cell",
+ "portable-atomic",
+ "pyo3-build-config",
+ "pyo3-ffi",
+ "pyo3-macros",
+ "unindent",
+]
+[[package]]
+name = "pyo3-build-config"
+version = "0.23.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "94f6cbe86ef3bf18998d9df6e0f3fc1050a8c5efa409bf712e661a4366e010fb"
+dependencies = [
+ "once_cell",
+ "target-lexicon",
+]
+[[package]]
+name = "pyo3-ffi"
+version = "0.23.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e9f1b4c431c0bb1c8fb0a338709859eed0d030ff6daa34368d3b152a63dfdd8d"
+dependencies = [
+ "libc",
+ "pyo3-build-config",
+]
+[[package]]
+name = "pyo3-macros"
+version = "0.23.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fbc2201328f63c4710f68abdf653c89d8dbc2858b88c5d88b0ff38a75288a9da"
+dependencies = [
+ "proc-macro2",
+ "pyo3-macros-backend",
+ "quote",
+ "syn 2.0.119",
+]
+[[package]]
+name = "pyo3-macros-backend"
+version = "0.23.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fca6726ad0f3da9c9de093d6f116a93c1a38e417ed73bf138472cf4064f72028"
+dependencies = [
+ "heck",
+ "proc-macro2",
+ "pyo3-build-config",
+ "quote",
+ "syn 2.0.119",
+]
+[[package]]
+name = "quick-error"
+version = "1.2.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
+[[package]]
+name = "quote"
+version = "1.0.47"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1fbf4db142a473a8d80c26bbf18454ed458bf8d26c8219c331daecfdbd079001"
+dependencies = [
+ "proc-macro2",
+]
+[[package]]
+name = "r-efi"
+version = "6.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f8dcc9c7d52a811697d2151c701e0d08956f92b0e24136cf4cf27b57a6a0d9bf"
+[[package]]
+name = "regex"
+version = "1.13.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f020237b6c8eed93db2e2cb53c00c60a8e1bc73da7d073199a1180401450218d"
+dependencies = [
+ "aho-corasick",
+ "memchr",
+ "regex-automata",
+ "regex-syntax",
+]
+[[package]]
+name = "regex-automata"
+version = "0.4.18"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ad8553b9b26413251cbf30e620595c7a41b3887f03da04579c0e6b0d6a06b4b2"
+dependencies = [
+ "aho-corasick",
+ "memchr",
+ "regex-syntax",
+]
+[[package]]
+name = "regex-syntax"
+version = "0.8.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d6f6ff9a378485b298a5286656da665ba74413d36db0979633275d2e708145d4"
+[[package]]
+name = "rust-htslib"
+version = "0.47.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f62b46e47d8b025589565f0eefe83e8646faf0faf74d17014b1b6ea2c1504930"
+dependencies = [
+ "bio-types",
+ "byteorder",
+ "custom_derive",
+ "derive-new 0.5.9",
+ "hts-sys",
+ "ieee754",
+ "lazy_static",
+ "libc",
+ "libz-sys",
+ "linear-map",
+ "newtype_derive",
+ "regex",
+ "thiserror 1.0.69",
+ "url",
+]
+[[package]]
+name = "rustc-hash"
+version = "2.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6b1e7f9a428571be2dc5bc0505c13fb6bf936822b894ec87abf8a08a4e51742d"
+[[package]]
+name = "rustc_version"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084"
+dependencies = [
+ "semver",
+]
+[[package]]
+name = "rustversion"
+version = "1.0.23"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cf54715a573b99ac80df0bc206da022bcd442c974952c7b9720069370852e21f"
+[[package]]
+name = "semver"
+version = "0.1.20"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
+[[package]]
+name = "serde"
+version = "1.0.229"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4148590afebada386688f18773da617792bf2ef03ffc1e4cbd2b1d45b023e0ba"
+dependencies = [
+ "serde_core",
+ "serde_derive",
+]
+[[package]]
+name = "serde_core"
+version = "1.0.229"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "67dca2c9c51e58a4791a4b1ed58308b39c64224d349a935ab5039aa360942a48"
+dependencies = [
+ "serde_derive",
+]
+[[package]]
+name = "serde_derive"
+version = "1.0.229"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e7a5d71263a5a7d47b41f6b3f06ba276f10cc18b0931f1799f710578e2309348"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 3.0.3",
+]
+[[package]]
+name = "serde_json"
+version = "1.0.151"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c841b55ecdae098c80dcae9cf767f6f8a0c2cdb3416bbef72181df4d0fe73f14"
+dependencies = [
+ "itoa",
+ "memchr",
+ "serde",
+ "serde_core",
+ "zmij",
+]
+[[package]]
+name = "sha2"
+version = "0.10.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a7507d819769d01a365ab707794a4084392c824f54a7a6a7862f8c3d0892b283"
+dependencies = [
+ "cfg-if",
+ "cpufeatures",
+ "digest",
+]
+[[package]]
+name = "shlex"
+version = "1.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
+[[package]]
+name = "shlex"
+version = "2.0.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f8fadd59c855ef2080decdef8ff161eb6661b86933c9d82e5ba29dc602a55aba"
+[[package]]
+name = "smallvec"
+version = "1.15.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8ed6a63f02c8539c91a8685a86f4099661ba3da017932f6ebbea6de3f0fa7c90"
+[[package]]
+name = "stable_deref_trait"
+version = "1.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6ce2be8dc25455e1f91df71bfa12ad37d7af1092ae736f3a6cd0e37bc7810596"
+[[package]]
+name = "strum_macros"
+version = "0.26.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4c6bee85a5a24955dc440386795aa378cd9cf82acd5f764469152d2270e581be"
+dependencies = [
+ "heck",
+ "proc-macro2",
+ "quote",
+ "rustversion",
+ "syn 2.0.119",
+]
+[[package]]
+name = "syn"
+version = "1.0.109"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+[[package]]
+name = "syn"
+version = "2.0.119"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "872831b642d1a07999a962a351ed35b955ea2cfc8f3862091e2a240a84f17297"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+[[package]]
+name = "syn"
+version = "3.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "53e9bae58849f64dfa4f5d5ae372c8341f7305f82a3868709269343628b659a3"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "unicode-ident",
+]
+[[package]]
+name = "synstructure"
+version = "0.13.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "728a70f3dbaf5bab7f0c4b1ac8d7ae5ea60a4b5549c8a5914361c99147a709d2"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.119",
+]
+[[package]]
+name = "target-lexicon"
+version = "0.12.16"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1"
+[[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 = "2.0.20"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ec86235f5fcc2a73650310756d2ac5b138a5780bbbdfae3eeccec992c435ba4f"
+dependencies = [
+ "thiserror-impl 2.0.20",
+]
+[[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 2.0.119",
+]
+[[package]]
+name = "thiserror-impl"
+version = "2.0.20"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bc04cd3e1236dd4a98afca4569f2deb3f120e5422a4023be2cb683f8486292af"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 3.0.3",
+]
+[[package]]
+name = "tinystr"
+version = "0.8.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b1e27c91459209c2986af3dcf603a5a74a4368754ce37414f59acc971167f643"
+dependencies = [
+ "displaydoc",
+ "zerovec",
+]
+[[package]]
+name = "txnova-core"
+version = "0.1.0"
+dependencies = [
+ "pyo3",
+ "rust-htslib",
+ "serde",
+ "serde_json",
+ "sha2",
+ "thiserror 2.0.20",
+]
+[[package]]
+name = "typenum"
+version = "1.20.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b6f5e870be6c3b371b77fe0ee0bafb859fa4964b4404c27de1d380043c4dda20"
+[[package]]
+name = "unicode-ident"
+version = "1.0.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e6e4313cd5fcd3dad5cafa179702e2b244f760991f45397d14d4ebf38247da75"
+[[package]]
+name = "unindent"
+version = "0.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7264e107f553ccae879d21fbea1d6724ac785e8c3bfc762137959b5802826ef3"
+[[package]]
+name = "url"
+version = "2.5.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ff67a8a4397373c3ef660812acab3268222035010ab8680ec4215f38ba3d0eed"
+dependencies = [
+ "form_urlencoded",
+ "idna",
+ "percent-encoding",
+ "serde",
+]
+[[package]]
+name = "utf8_iter"
+version = "1.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b6c140620e7ffbb22c2dee59cafe6084a59b5ffc27a8859a5f0d494b5d52b6be"
+[[package]]
+name = "vcpkg"
+version = "0.2.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
+[[package]]
+name = "version_check"
+version = "0.9.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a"
+[[package]]
+name = "windows-link"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f0805222e57f7521d6a62e36fa9163bc891acd422f971defe97d64e70d0a4fe5"
+[[package]]
+name = "writeable"
+version = "0.6.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3ad82d2a33cdc9674dc7465672f271e096168fcdbe0f799d9e6db8c5892679dc"
+[[package]]
+name = "yoke"
+version = "0.8.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "709fe23a0424b6a435d82152b1bd3fdfb0833487d5fa90d05d42762a9891fef5"
+dependencies = [
+ "stable_deref_trait",
+ "yoke-derive",
+ "zerofrom",
+]
+[[package]]
+name = "yoke-derive"
+version = "0.8.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "de844c262c8848816172cef550288e7dc6c7b7814b4ee56b3e1553f275f1858e"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.119",
+ "synstructure",
+]
+[[package]]
+name = "zerofrom"
+version = "0.1.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0ec05a11813ea801ff6d75110ad09cd0824ddba17dfe17128ea0d5f68e6c5272"
+dependencies = [
+ "zerofrom-derive",
+]
+[[package]]
+name = "zerofrom-derive"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "11532158c46691caf0f2593ea8358fed6bbf68a0315e80aae9bd41fbade684a1"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.119",
+ "synstructure",
+]
+[[package]]
+name = "zerotrie"
+version = "0.2.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4ea269c3bd32f0a32c321907a2ae912ba6f4649bb0fc764a15627e99a7095a3f"
+dependencies = [
+ "displaydoc",
+ "yoke",
+ "zerofrom",
+]
+[[package]]
+name = "zerovec"
+version = "0.11.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "94b5c6b5976d66c1d703c4fd17d3f5e43c8cedaacf604961b171adc7130896d8"
+dependencies = [
+ "yoke",
+ "zerofrom",
+ "zerovec-derive",
+]
+[[package]]
+name = "zerovec-derive"
+version = "0.11.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "47402523226a02bfe5230160dc3ccc089aa6f6f19e7fcbb4e6f824bbb1b4aa62"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 3.0.3",
+]
+[[package]]
+name = "zmij"
+version = "1.0.23"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "29666d0abbfad1e3dc4dcf6144730dd3a3ab225bbbdac83319345b1b44ccfc1b"