version = 3
[[package]]
name = "ahash"
version = "0.7.6"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47"
dependencies = [
"getrandom",
"once_cell",
"version_check",
]
[[package]]
name = "aho-corasick"
version = "0.6.10"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "81ce3d38065e618af2d7b77e10c5ad9a069859b4be3c2250f674af3840d9c8a5"
dependencies = [
"memchr",
]
[[package]]
name = "approx"
version = "0.1.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "08abcc3b4e9339e33a3d0a5ed15d84a687350c05689d825e0f6655eef9e76a94"
[[package]]
name = "autocfg"
version = "1.1.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa"
[[package]]
name = "bio"
version = "0.20.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "0cce3355db216af27855806a62ec694774ed00775c6020f62705037b22cc18d8"
dependencies = [
"approx",
"bit-set",
"bv",
"bytecount",
"csv",
"custom_derive",
"fxhash",
"itertools 0.6.5",
"itertools-num",
"lazy_static 0.2.11",
"multimap",
"ndarray",
"newtype_derive",
"num-integer",
"num-traits 0.1.43",
"ordered-float",
"quick-error",
"regex",
"serde",
"serde_derive",
"vec_map",
]
[[package]]
name = "bit-set"
version = "0.4.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "d9bf6104718e80d7b26a68fdbacff3481cfc05df670821affc7e9cbc1884400c"
dependencies = [
"bit-vec",
]
[[package]]
name = "bit-vec"
version = "0.4.4"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "02b4ff8b16e6076c3e14220b39fbc1fabb6737522281a388998046859400895f"
[[package]]
name = "bstr"
version = "0.2.17"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "ba3569f383e8f1598449f1a423e72e99569137b47740b1da11ef19af3d5c3223"
dependencies = [
"lazy_static 1.4.0",
"memchr",
"regex-automata",
"serde",
]
[[package]]
name = "bv"
version = "0.7.4"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "d31c96a681465e7742cc04bb1961e732e21128bcf1dc9d5fe8cfc052b484f140"
dependencies = [
"serde",
]
[[package]]
name = "bytecount"
version = "0.3.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "f861d9ce359f56dbcb6e0c2a1cb84e52ad732cadb57b806adeb3c7668caccbd8"
[[package]]
name = "byteorder"
version = "1.4.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610"
[[package]]
name = "cfg-if"
version = "1.0.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
[[package]]
name = "csv"
version = "1.1.6"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "22813a6dc45b335f9bade10bf7271dc477e81113e89eb251a0bc2a8a81c536e1"
dependencies = [
"bstr",
"csv-core",
"itoa",
"ryu",
"serde",
]
[[package]]
name = "csv-core"
version = "0.1.10"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "2b2466559f260f48ad25fe6317b3c8dac77b5bdb5763ac7d9d6103530663bc90"
dependencies = [
"memchr",
]
[[package]]
name = "custom_derive"
version = "0.1.7"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9"
[[package]]
name = "either"
version = "1.7.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "3f107b87b6afc2a64fd13cac55fe06d6c8859f12d4b14cbcdd2c67d0976781be"
[[package]]
name = "fxhash"
version = "0.2.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "c31b6d751ae2c7f11320402d34e41349dd1016f8d5d45e48c4312bc8625af50c"
dependencies = [
"byteorder",
]
[[package]]
name = "getopts"
version = "0.2.21"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "14dbbfd5c71d70241ecf9e6f13737f7b5ce823821063188d7e46c41d371eebd5"
dependencies = [
"unicode-width",
]
[[package]]
name = "getrandom"
version = "0.2.7"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "4eb1a864a501629691edf6c15a593b7a51eebaa1e8468e9ddc623de7c9b58ec6"
dependencies = [
"cfg-if",
"libc",
"wasi 0.11.0+wasi-snapshot-preview1",
]
[[package]]
name = "hashbrown"
version = "0.12.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888"
dependencies = [
"ahash",
]
[[package]]
name = "hermit-abi"
version = "0.1.19"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33"
dependencies = [
"libc",
]
[[package]]
name = "itertools"
version = "0.6.5"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "d3f2be4da1690a039e9ae5fd575f706a63ad5a2120f161b1d653c9da3930dd21"
dependencies = [
"either",
]
[[package]]
name = "itertools"
version = "0.10.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "a9a9d19fa1e79b6215ff29b9d6880b706147f16e9b1dbb1e4e5947b5b02bc5e3"
dependencies = [
"either",
]
[[package]]
name = "itertools-num"
version = "0.1.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "a872a22f9e6f7521ca557660adb96dd830e54f0f490fa115bb55dd69d38b27e7"
dependencies = [
"num-traits 0.2.15",
]
[[package]]
name = "itoa"
version = "0.4.8"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "b71991ff56294aa922b450139ee08b3bfc70982c6b2c7562771375cf73542dd4"
[[package]]
name = "lazy_static"
version = "0.1.16"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "cf186d1a8aa5f5bee5fd662bc9c1b949e0259e1bcc379d1f006847b0080c7417"
[[package]]
name = "lazy_static"
version = "0.2.11"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "76f033c7ad61445c5b347c7382dd1237847eb1bce590fe50365dcb33d546be73"
[[package]]
name = "lazy_static"
version = "1.4.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
[[package]]
name = "libc"
version = "0.2.127"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "505e71a4706fa491e9b1b55f51b95d4037d0821ee40131190475f692b35b009b"
[[package]]
name = "matrixmultiply"
version = "0.1.15"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "dcad67dcec2d58ff56f6292582377e6921afdf3bfbd533e26fb8900ae575e002"
dependencies = [
"rawpointer",
]
[[package]]
name = "memchr"
version = "2.5.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d"
[[package]]
name = "multimap"
version = "0.4.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "2eb04b9f127583ed176e163fb9ec6f3e793b87e21deedd5734a69386a18a0151"
dependencies = [
"serde",
]
[[package]]
name = "ndarray"
version = "0.9.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "9d0603e041601804a61a33ebecbea220b43a86437b9ee20680a1f9fdaaa922a8"
dependencies = [
"itertools 0.6.5",
"matrixmultiply",
"num-complex 0.1.43",
"num-traits 0.1.43",
]
[[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 = "num"
version = "0.3.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "8b7a8e9be5e039e2ff869df49155f1c06bd01ade2117ec783e56ab0932b67a8f"
dependencies = [
"num-bigint",
"num-complex 0.3.1",
"num-integer",
"num-iter",
"num-rational",
"num-traits 0.2.15",
]
[[package]]
name = "num-bigint"
version = "0.3.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "5f6f7833f2cbf2360a6cfd58cd41a53aa7a90bd4c202f5b1c7dd2ed73c57b2c3"
dependencies = [
"autocfg",
"num-integer",
"num-traits 0.2.15",
]
[[package]]
name = "num-complex"
version = "0.1.43"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "b288631d7878aaf59442cffd36910ea604ecd7745c36054328595114001c9656"
dependencies = [
"num-traits 0.2.15",
]
[[package]]
name = "num-complex"
version = "0.3.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "747d632c0c558b87dbabbe6a82f3b4ae03720d0646ac5b7b4dae89394be5f2c5"
dependencies = [
"num-traits 0.2.15",
]
[[package]]
name = "num-integer"
version = "0.1.45"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9"
dependencies = [
"autocfg",
"num-traits 0.2.15",
]
[[package]]
name = "num-iter"
version = "0.1.43"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "7d03e6c028c5dc5cac6e2dec0efda81fc887605bb3d884578bb6d6bf7514e252"
dependencies = [
"autocfg",
"num-integer",
"num-traits 0.2.15",
]
[[package]]
name = "num-rational"
version = "0.3.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "12ac428b1cb17fce6f731001d307d351ec70a6d202fc2e60f7d4c5e42d8f4f07"
dependencies = [
"autocfg",
"num-bigint",
"num-integer",
"num-traits 0.2.15",
]
[[package]]
name = "num-traits"
version = "0.1.43"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "92e5113e9fd4cc14ded8e499429f396a20f98c772a47cc8622a736e1ec843c31"
dependencies = [
"num-traits 0.2.15",
]
[[package]]
name = "num-traits"
version = "0.2.15"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd"
dependencies = [
"autocfg",
]
[[package]]
name = "num_cpus"
version = "1.13.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "19e64526ebdee182341572e50e9ad03965aa510cd94427a4549448f285e957a1"
dependencies = [
"hermit-abi",
"libc",
]
[[package]]
name = "once_cell"
version = "1.13.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "18a6dbe30758c9f83eb00cbea4ac95966305f5a7772f3f42ebfc7fc7eddbd8e1"
[[package]]
name = "ordered-float"
version = "0.5.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "7eb5259643245d3f292c7a146b2df53bba24d7eab159410e648eb73dc164669d"
dependencies = [
"num-traits 0.1.43",
"unreachable",
]
[[package]]
name = "proc-macro2"
version = "1.0.43"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "0a2ca2c61bc9f3d74d2886294ab7b9853abd9c1ad903a3ac7815c58989bb7bab"
dependencies = [
"unicode-ident",
]
[[package]]
name = "quick-error"
version = "1.2.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
[[package]]
name = "quote"
version = "1.0.21"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "bbe448f377a7d6961e30f5955f9b8d106c3f5e449d493ee1b125c1d43c2b5179"
dependencies = [
"proc-macro2",
]
[[package]]
name = "rawpointer"
version = "0.1.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "ebac11a9d2e11f2af219b8b8d833b76b1ea0e054aa0e8d8e9e4cbde353bdf019"
[[package]]
name = "regex"
version = "0.2.11"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "9329abc99e39129fcceabd24cf5d85b4671ef7c29c50e972bc5afe32438ec384"
dependencies = [
"aho-corasick",
"memchr",
"regex-syntax",
"thread_local",
"utf8-ranges",
]
[[package]]
name = "regex-automata"
version = "0.1.10"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132"
[[package]]
name = "regex-syntax"
version = "0.5.6"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "7d707a4fa2637f2dca2ef9fd02225ec7661fe01a53623c1e6515b6916511f7a7"
dependencies = [
"ucd-util",
]
[[package]]
name = "rna-algos"
version = "0.1.33"
dependencies = [
"bio",
"getopts",
"hashbrown",
"itertools 0.10.3",
"lazy_static 0.1.16",
"num",
"num_cpus",
"rna-ss-params",
"scoped_threadpool",
"time",
]
[[package]]
name = "rna-ss-params"
version = "0.1.22"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "f775aae71830453f56e2abaac5d294c0996fc4666092f9ec72d316caaff0623d"
dependencies = [
"getopts",
"lazy_static 0.1.16",
]
[[package]]
name = "rustc_version"
version = "0.1.7"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084"
dependencies = [
"semver",
]
[[package]]
name = "ryu"
version = "1.0.11"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "4501abdff3ae82a1c1b477a17252eb69cee9e66eb915c1abaa4f44d873df9f09"
[[package]]
name = "scoped_threadpool"
version = "0.1.9"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "1d51f5df5af43ab3f1360b429fa5e0152ac5ce8c0bd6485cae490332e96846a8"
[[package]]
name = "semver"
version = "0.1.20"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
[[package]]
name = "serde"
version = "1.0.142"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "e590c437916fb6b221e1d00df6e3294f3fccd70ca7e92541c475d6ed6ef5fee2"
dependencies = [
"serde_derive",
]
[[package]]
name = "serde_derive"
version = "1.0.142"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "34b5b8d809babe02f538c2cfec6f2c1ed10804c0e5a6a041a049a4f5588ccc2e"
dependencies = [
"proc-macro2",
"quote",
"syn",
]
[[package]]
name = "syn"
version = "1.0.99"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "58dbef6ec655055e20b86b15a8cc6d439cca19b667537ac6a1369572d151ab13"
dependencies = [
"proc-macro2",
"quote",
"unicode-ident",
]
[[package]]
name = "thread_local"
version = "0.3.6"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "c6b53e329000edc2b34dbe8545fd20e55a333362d0a321909685a19bd28c3f1b"
dependencies = [
"lazy_static 1.4.0",
]
[[package]]
name = "time"
version = "0.1.44"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "6db9e6914ab8b1ae1c260a4ae7a49b6c5611b40328a735b21862567685e73255"
dependencies = [
"libc",
"wasi 0.10.0+wasi-snapshot-preview1",
"winapi",
]
[[package]]
name = "ucd-util"
version = "0.1.9"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "65bfcbf611b122f2c10eb1bb6172fbc4c2e25df9970330e4d75ce2b5201c9bfc"
[[package]]
name = "unicode-ident"
version = "1.0.3"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "c4f5b37a154999a8f3f98cc23a628d850e154479cd94decf3414696e12e31aaf"
[[package]]
name = "unicode-width"
version = "0.1.9"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "3ed742d4ea2bd1176e236172c8429aaf54486e7ac098db29ffe6529e0ce50973"
[[package]]
name = "unreachable"
version = "1.0.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "382810877fe448991dfc7f0dd6e3ae5d58088fd0ea5e35189655f84e6814fa56"
dependencies = [
"void",
]
[[package]]
name = "utf8-ranges"
version = "1.0.5"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "7fcfc827f90e53a02eaef5e535ee14266c1d569214c6aa70133a624d8a3164ba"
[[package]]
name = "vec_map"
version = "0.8.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "f1bddf1187be692e79c5ffeab891132dfb0f236ed36a43c7ed39f1165ee20191"
dependencies = [
"serde",
]
[[package]]
name = "version_check"
version = "0.9.4"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
[[package]]
name = "void"
version = "1.0.2"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "6a02e4885ed3bc0f2de90ea6dd45ebcbb66dacffe03547fadbb0eeae2770887d"
[[package]]
name = "wasi"
version = "0.10.0+wasi-snapshot-preview1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "1a143597ca7c7793eff794def352d41792a93c481eb1042423ff7ff72ba2c31f"
[[package]]
name = "wasi"
version = "0.11.0+wasi-snapshot-preview1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
[[package]]
name = "winapi"
version = "0.3.9"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419"
dependencies = [
"winapi-i686-pc-windows-gnu",
"winapi-x86_64-pc-windows-gnu",
]
[[package]]
name = "winapi-i686-pc-windows-gnu"
version = "0.4.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
[[package]]
name = "winapi-x86_64-pc-windows-gnu"
version = "0.4.0"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f"