diff --git a/polbin/Cargo.lock b/polbin/Cargo.lock index a2620a1e..cd09d52a 100644 --- a/polbin/Cargo.lock +++ b/polbin/Cargo.lock @@ -2,21 +2,6 @@ # It is not intended for manual editing. version = 3 -[[package]] -name = "aho-corasick" -version = "1.1.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0" -dependencies = [ - "memchr", -] - -[[package]] -name = "anyhow" -version = "1.0.80" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5ad32ce52e4161730f7098c077cd2ed6229b5804ccf99e5366be1ab72a98b4e1" - [[package]] name = "argh" version = "0.1.12" @@ -48,27 +33,6 @@ dependencies = [ "serde", ] -[[package]] -name = "arrayvec" -version = "0.5.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "23b62fc65de8e4e7f52534fb52b0f3ed04746ae267519eef2a83941e8085068b" - -[[package]] -name = "bitflags" -version = "1.3.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" - -[[package]] -name = "bstr" -version = "0.2.17" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ba3569f383e8f1598449f1a423e72e99569137b47740b1da11ef19af3d5c3223" -dependencies = [ - "memchr", -] - [[package]] name = "bstr" version = "1.9.1" @@ -80,66 +44,18 @@ dependencies = [ "serde", ] -[[package]] -name = "bytemuck" -version = "1.14.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a2ef034f05691a48569bd920a96c81b9d91bbad1ab5ac7c4616c1f6ef36cb79f" -dependencies = [ - "bytemuck_derive", -] - -[[package]] -name = "bytemuck_derive" -version = "1.5.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "965ab7eb5f8f97d2a083c799f3a1b994fc397b2fe2da5d1da1626ce15a39f2b1" -dependencies = [ - "proc-macro2", - "quote", - "syn", -] - [[package]] name = "byteorder" version = "1.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b" -[[package]] -name = "cfg-if" -version = "1.0.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" - [[package]] name = "equivalent" version = "1.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5" -[[package]] -name = "fnv" -version = "1.0.7" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1" - -[[package]] -name = "gfa" -version = "0.10.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9632601a032d2ae43f5050b454dd27c2add69b2e52bd46a4888f3aeb6e3629f5" -dependencies = [ - "anyhow", - "bstr 0.2.17", - "bytemuck", - "fnv", - "lazy_static", - "memmap", - "nom", - "regex", -] - [[package]] name = "hashbrown" version = "0.14.3" @@ -156,25 +72,6 @@ dependencies = [ "hashbrown", ] -[[package]] -name = "lazy_static" -version = "1.4.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646" - -[[package]] -name = "lexical-core" -version = "0.7.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6607c62aa161d23d17a9072cc5da0be67cdfc89d3afb1e8d9c842bebc2525ffe" -dependencies = [ - "arrayvec", - "bitflags", - "cfg-if", - "ryu", - "static_assertions", -] - [[package]] name = "libc" version = "0.2.153" @@ -197,17 +94,6 @@ dependencies = [ "winapi", ] -[[package]] -name = "nom" -version = "5.1.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "08959a387a676302eebf4ddbcbc611da04285579f76f88ee0506c63b1a61dd4b" -dependencies = [ - "lexical-core", - "memchr", - "version_check", -] - [[package]] name = "num_enum" version = "0.7.2" @@ -234,8 +120,7 @@ name = "polbin" version = "0.1.0" dependencies = [ "argh", - "bstr 1.9.1", - "gfa", + "bstr", "memmap", "num_enum", "zerocopy", @@ -268,40 +153,11 @@ dependencies = [ "proc-macro2", ] -[[package]] -name = "regex" -version = "1.10.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b62dbe01f0b06f9d8dc7d49e05a0785f153b00b2c227856282f671e0318c9b15" -dependencies = [ - "aho-corasick", - "memchr", - "regex-automata", - "regex-syntax", -] - [[package]] name = "regex-automata" version = "0.4.6" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "86b83b8b9847f9bf95ef68afb0b8e6cdb80f498442f5179a29fad448fcc1eaea" -dependencies = [ - "aho-corasick", - "memchr", - "regex-syntax", -] - -[[package]] -name = "regex-syntax" -version = "0.8.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f" - -[[package]] -name = "ryu" -version = "1.0.17" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1" [[package]] name = "serde" @@ -323,12 +179,6 @@ dependencies = [ "syn", ] -[[package]] -name = "static_assertions" -version = "1.1.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f" - [[package]] name = "syn" version = "2.0.52" @@ -363,12 +213,6 @@ version = "1.0.12" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b" -[[package]] -name = "version_check" -version = "0.9.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f" - [[package]] name = "winapi" version = "0.3.9" diff --git a/polbin/Cargo.toml b/polbin/Cargo.toml index 4ca5c863..b3dba9f6 100644 --- a/polbin/Cargo.toml +++ b/polbin/Cargo.toml @@ -6,7 +6,6 @@ edition = "2021" [dependencies] argh = "0.1.12" bstr = "1.9.1" -gfa = "0.10.1" memmap = "0.7.0" num_enum = "0.7.2" zerocopy = { version = "0.7.32", features = ["derive"] } diff --git a/polbin/src/gfaline.rs b/polbin/src/gfaline.rs index 0a2719d3..047224b8 100644 --- a/polbin/src/gfaline.rs +++ b/polbin/src/gfaline.rs @@ -210,10 +210,6 @@ fn parse_align(s: &[u8]) -> PartialParseResult> { } /// Parse GFA paths' segment lists. These look like `1+,2-,3+`. -/// -/// The underlying gfa-rs library does not yet parse the actual segments -/// involved in the path. So we do it ourselves: splitting on commas and -/// matching the direction. pub struct StepsParser<'a> { str: &'a [u8], index: usize,