diff --git a/Cargo.lock b/Cargo.lock index 1272423..44ab257 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -10,9 +10,9 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" [[package]] name = "aho-corasick" -version = "0.7.18" +version = "1.0.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1e37cfd5e7657ada45f742d6e99ca5788580b5c529dc78faf11ece6dc702656f" +checksum = "6748e8def348ed4d14996fa801f4122cd763fff530258cdc03f64b25f89d3a5a" dependencies = [ "memchr", ] @@ -28,9 +28,9 @@ dependencies = [ [[package]] name = "anyhow" -version = "1.0.58" +version = "1.0.75" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bb07d2053ccdbe10e2af2995a2f116c1330396493dc1269f6a91d0ae82e19704" +checksum = "a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6" [[package]] name = "atty" @@ -38,7 +38,7 @@ version = "0.2.14" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8" dependencies = [ - "hermit-abi", + "hermit-abi 0.1.19", "libc", "winapi 0.3.9", ] @@ -55,6 +55,12 @@ version = "1.3.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" +[[package]] +name = "bitflags" +version = "2.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b4682ae6287fcf752ecaabbfcc7b6f9b72aa33933dc23a554d853aea8eea8635" + [[package]] name = "bitvec" version = "1.0.1" @@ -75,15 +81,14 @@ checksum = "ba3569f383e8f1598449f1a423e72e99569137b47740b1da11ef19af3d5c3223" dependencies = [ "lazy_static", "memchr", - "regex-automata", - "serde", + "regex-automata 0.1.10", ] [[package]] -name = "buf_redux" -version = "0.8.4" +name = "buffer-redux" +version = "1.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b953a6887648bb07a535631f2bc00fbdb2a2216f135552cb3f534ed136b9c07f" +checksum = "d2886ea01509598caac116942abd33ab5a88fa32acdf7e4abfa0fc489ca520c9" dependencies = [ "memchr", "safemem", @@ -91,9 +96,9 @@ dependencies = [ [[package]] name = "built" -version = "0.5.1" +version = "0.5.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4f346b6890a0dfa7266974910e7df2d5088120dd54721b9b0e5aae1ae5e05715" +checksum = "5b9c056b9ed43aee5e064b683aa1ec783e19c6acec7559e3ae931b7490472fbe" dependencies = [ "cargo-lock", "git2", @@ -101,9 +106,9 @@ dependencies = [ [[package]] name = "bumpalo" -version = "3.10.0" +version = "3.13.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "37ccbd214614c6783386c1af30caf03192f17891059cecc394b4fb119e363de3" +checksum = "a3e2c3daef883ecc1b5d58c15adae93470a91d425f3532ba1695849656af3fc1" [[package]] name = "byteorder" @@ -113,15 +118,15 @@ checksum = "14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610" [[package]] name = "bytes" -version = "1.2.1" +version = "1.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ec8a7b6a70fde80372154c65702f00a0f56f3e1c36abbc6c440484be248856db" +checksum = "89b2fd2a0dcf38d7971e2194b6b6eebab45ae01067456a7fd93d5547a61b70be" [[package]] name = "cargo-lock" -version = "7.1.0" +version = "8.0.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6c408da54db4c50d4693f7e649c299bc9de9c23ead86249e5368830bb32a734b" +checksum = "031718ddb8f78aa5def78a09e90defe30151d1f6c672f937af4dd916429ed996" dependencies = [ "semver", "serde", @@ -131,11 +136,12 @@ dependencies = [ [[package]] name = "cc" -version = "1.0.73" +version = "1.0.82" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2fff2a6927b3bb87f9595d67196a70493f627687a71d87a0d692242c33f58c11" +checksum = "305fe645edc1442a0fa8b6726ba61d422798d37a52e12eaecf4b022ebbb88f01" dependencies = [ "jobserver", + "libc", ] [[package]] @@ -158,7 +164,7 @@ checksum = "a0610544180c38b88101fecf2dd634b174a62eef6946f84dfc6a7127512b381c" dependencies = [ "ansi_term", "atty", - "bitflags", + "bitflags 1.3.2", "strsim", "textwrap", "unicode-width", @@ -167,9 +173,9 @@ dependencies = [ [[package]] name = "cmake" -version = "0.1.48" +version = "0.1.50" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e8ad8cef104ac57b68b89df3208164d228503abbdce70f6880ffa3d970e7443a" +checksum = "a31c789563b815f77f4250caee12365734369f942439b7defd71e18a48197130" dependencies = [ "cc", ] @@ -195,25 +201,11 @@ dependencies = [ "cfg-if 1.0.0", ] -[[package]] -name = "crossbeam" -version = "0.8.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2801af0d36612ae591caa9568261fddce32ce6e08a7275ea334a06a4ad021a2c" -dependencies = [ - "cfg-if 1.0.0", - "crossbeam-channel", - "crossbeam-deque", - "crossbeam-epoch", - "crossbeam-queue", - "crossbeam-utils", -] - [[package]] name = "crossbeam-channel" -version = "0.5.6" +version = "0.5.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c2dd04ddaf88237dc3b8d8f9a3c1004b506b54b3313403944054d23c0870c521" +checksum = "a33c2bf77f2df06183c3aa30d1e96c0695a313d4f9c453cc3762a6db39f99200" dependencies = [ "cfg-if 1.0.0", "crossbeam-utils", @@ -221,9 +213,9 @@ dependencies = [ [[package]] name = "crossbeam-deque" -version = "0.8.2" +version = "0.8.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "715e8152b692bba2d374b53d4875445368fdf21a94751410af607a5ac677d1fc" +checksum = "ce6fd6f855243022dcecf8702fef0c297d4338e226845fe067f6341ad9fa0cef" dependencies = [ "cfg-if 1.0.0", "crossbeam-epoch", @@ -232,45 +224,32 @@ dependencies = [ [[package]] name = "crossbeam-epoch" -version = "0.9.10" +version = "0.9.15" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "045ebe27666471bb549370b4b0b3e51b07f56325befa4284db65fc89c02511b1" +checksum = "ae211234986c545741a7dc064309f67ee1e5ad243d0e48335adc0484d960bcc7" dependencies = [ "autocfg", "cfg-if 1.0.0", "crossbeam-utils", "memoffset", - "once_cell", "scopeguard", ] -[[package]] -name = "crossbeam-queue" -version = "0.3.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1cd42583b04998a5363558e5f9291ee5a5ff6b49944332103f251e7479a82aa7" -dependencies = [ - "cfg-if 1.0.0", - "crossbeam-utils", -] - [[package]] name = "crossbeam-utils" -version = "0.8.11" +version = "0.8.16" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "51887d4adc7b564537b15adcfb307936f8075dfcd5f00dde9a9f1d29383682bc" +checksum = "5a22b2d63d4d1dc0b7f1b6b2747dd0088008a9be28b6ddf0b1e7d335e3037294" dependencies = [ "cfg-if 1.0.0", - "once_cell", ] [[package]] name = "csv" -version = "1.1.6" +version = "1.2.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "22813a6dc45b335f9bade10bf7271dc477e81113e89eb251a0bc2a8a81c536e1" +checksum = "626ae34994d3d8d668f4269922248239db4ae42d538b14c398b74a52208e8086" dependencies = [ - "bstr", "csv-core", "itoa", "ryu", @@ -288,15 +267,15 @@ dependencies = [ [[package]] name = "either" -version = "1.7.0" +version = "1.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3f107b87b6afc2a64fd13cac55fe06d6c8859f12d4b14cbcdd2c67d0976781be" +checksum = "a26ae43d7bcc3b814de94796a5e736d4029efb0ee900c12e2d54c993ad1a1e07" [[package]] name = "env_logger" -version = "0.9.0" +version = "0.9.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0b2cf0344971ee6c64c31be0d530793fba457d322dfec2810c453d0ef228f9c3" +checksum = "a12e6657c4c97ebab115a42dcee77225f7f482cdd841cf7088c657a42e9e00e7" dependencies = [ "atty", "humantime", @@ -306,31 +285,49 @@ dependencies = [ ] [[package]] -name = "fastrand" -version = "1.8.0" +name = "errno" +version = "0.3.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a7a407cfaa3385c4ae6b23e84623d48c2798d06e3e6a1878f7f59f17b3f86499" +checksum = "6b30f669a7961ef1631673d2766cc92f52d64f7ef354d4fe0ddfd30ed52f0f4f" dependencies = [ - "instant", + "errno-dragonfly", + "libc", + "windows-sys", ] [[package]] -name = "fgoxide" -version = "0.1.3" +name = "errno-dragonfly" +version = "0.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf" +dependencies = [ + "cc", + "libc", +] + +[[package]] +name = "fastrand" +version = "2.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d571c2c4fb6b56ada5b136196eb40aa4b4e22ae7ca2efb7eb2f8d45e6c13c297" +checksum = "6999dc1837253364c2ebb0704ba97994bd874e8f195d665c50b7548f6ea92764" + +[[package]] +name = "fgoxide" +version = "0.3.0" +source = "git+https://github.com/kockan/fgoxide#7b35638d58905bd04a1429401dd92cd85f765b81" dependencies = [ "csv", "flate2", "serde", "thiserror", + "zstd", ] [[package]] name = "flate2" -version = "1.0.24" +version = "1.0.27" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f82b0f4c27ad9f8bfd1f3208d882da2b09c301bc1c828fd3a00d0216d2fbbff6" +checksum = "c6c98ee8095e9d1dcbf2fcc6d95acccb90d1c81db1e44725c6a984b1dbdfb010" dependencies = [ "crc32fast", "libz-sys", @@ -352,11 +349,10 @@ dependencies = [ [[package]] name = "form_urlencoded" -version = "1.0.1" +version = "1.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5fc25a87fa4fd2094bffb06925852034d90a17f0d1e05197d4956d3555752191" +checksum = "a62bc1cf6f830c2ec14a513a9fb124d0a213a629668a4186f329db21fe045652" dependencies = [ - "matches", "percent-encoding", ] @@ -390,6 +386,7 @@ dependencies = [ "serde", "structopt", "tempfile", + "zstd", ] [[package]] @@ -400,21 +397,21 @@ checksum = "e6d5a32815ae3f33302d95fdcb2ce17862f8c65363dcfd29360480ba1001fc9c" [[package]] name = "futures-core" -version = "0.3.21" +version = "0.3.28" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0c09fd04b7e4073ac7156a9539b57a484a8ea920f79c7c675d05d289ab6110d3" +checksum = "4bca583b7e26f571124fe5b7561d49cb2868d79116cfa0eefce955557c6fee8c" [[package]] name = "futures-sink" -version = "0.3.21" +version = "0.3.28" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "21163e139fa306126e6eedaf49ecdb4588f939600f0b1e770f4205ee4b7fa868" +checksum = "f43be4fe21a13b9781a69afa4985b0f6ee0e1afab2c6f454a8cf30e2b2237b6e" [[package]] name = "getrandom" -version = "0.2.7" +version = "0.2.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4eb1a864a501629691edf6c15a593b7a51eebaa1e8468e9ddc623de7c9b58ec6" +checksum = "be4136b2a15dd319360be1c07d9933517ccf0be8f16bf62a3bee4f0d618df427" dependencies = [ "cfg-if 1.0.0", "js-sys", @@ -425,11 +422,11 @@ dependencies = [ [[package]] name = "git2" -version = "0.13.25" +version = "0.15.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f29229cc1b24c0e6062f6e742aa3e256492a5323365e5ed3413599f8a5eff7d6" +checksum = "2994bee4a3a6a51eb90c218523be382fd7ea09b16380b9312e9dbe955ff7c7d1" dependencies = [ - "bitflags", + "bitflags 1.3.2", "libc", "libgit2-sys", "log", @@ -471,6 +468,12 @@ dependencies = [ "libc", ] +[[package]] +name = "hermit-abi" +version = "0.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "443144c8cdadd93ebf52ddb4056d257f5b52c04d3c804e657d19eb73fc33668b" + [[package]] name = "humantime" version = "2.1.0" @@ -479,11 +482,10 @@ checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4" [[package]] name = "idna" -version = "0.2.3" +version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "418a0a6fab821475f634efe3ccc45c013f742efe03d853e8d3355d5cb850ecf8" +checksum = "7d20d6b07bfbc108882d88ed8e37d39636dcc260e15e30c45e6ba089610b917c" dependencies = [ - "matches", "unicode-bidi", "unicode-normalization", ] @@ -511,33 +513,33 @@ dependencies = [ [[package]] name = "itertools" -version = "0.10.3" +version = "0.10.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a9a9d19fa1e79b6215ff29b9d6880b706147f16e9b1dbb1e4e5947b5b02bc5e3" +checksum = "b0fd2260e829bddf4cb6ea802289de2f86d6a7a690192fbe91b3f46e0f2c8473" dependencies = [ "either", ] [[package]] name = "itoa" -version = "0.4.8" +version = "1.0.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b71991ff56294aa922b450139ee08b3bfc70982c6b2c7562771375cf73542dd4" +checksum = "af150ab688ff2122fcef229be89cb50dd66af9e01a4ff320cc137eecc9bacc38" [[package]] name = "jobserver" -version = "0.1.24" +version = "0.1.26" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "af25a77299a7f711a01975c35a6a424eb6862092cc2d6c72c4ed6cbc56dfc1fa" +checksum = "936cfd212a0155903bcbc060e316fb6cc7cbf2e1907329391ebadc1fe0ce77c2" dependencies = [ "libc", ] [[package]] name = "js-sys" -version = "0.3.59" +version = "0.3.64" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "258451ab10b34f8af53416d1fdab72c22e805f0c92a1136d59470ec0b11138b2" +checksum = "c5f195fe497f702db0f318b07fdd68edb16955aed830df8363d837542f8f935a" dependencies = [ "wasm-bindgen", ] @@ -560,9 +562,9 @@ checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646" [[package]] name = "libc" -version = "0.2.126" +version = "0.2.147" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "349d5a591cd28b49e1d1037471617a32ddcda5731b99419008085f72d5a53836" +checksum = "b4668fb0ea861c1df094127ac5f1da3409a82116a4ba74fca2e58ef927159bb3" [[package]] name = "libdeflate-sys" @@ -584,9 +586,9 @@ dependencies = [ [[package]] name = "libgit2-sys" -version = "0.12.26+1.3.0" +version = "0.14.2+1.5.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "19e1c899248e606fbfe68dcb31d8b0176ebab833b103824af31bddf4b7457494" +checksum = "7f3d95f6b51075fe9810a7ae22c7095f12b98005ab364d8544797a825ce946a4" dependencies = [ "cc", "libc", @@ -596,18 +598,19 @@ dependencies = [ [[package]] name = "libmimalloc-sys" -version = "0.1.25" +version = "0.1.33" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "11ca136052550448f55df7898c6dbe651c6b574fe38a0d9ea687a9f8088a2e2c" +checksum = "f4ac0e912c8ef1b735e92369695618dc5b1819f5a7bf3f167301a3ba1cea515e" dependencies = [ "cc", + "libc", ] [[package]] name = "libz-sys" -version = "1.1.8" +version = "1.1.12" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9702761c3935f8cc2f101793272e202c72b99da8f4224a19ddcf1279a6450bbf" +checksum = "d97137b25e321a73eef1418d1d5d2eda4d77e12813f8e6dead84bc52c5870a7b" dependencies = [ "cc", "cmake", @@ -616,11 +619,17 @@ dependencies = [ "vcpkg", ] +[[package]] +name = "linux-raw-sys" +version = "0.4.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "57bcfdad1b858c2db7c38303a6d2ad4dfaf5eb53dfeb0910128b2c26d6158503" + [[package]] name = "lock_api" -version = "0.4.7" +version = "0.4.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "327fa5b6a6940e4699ec49a9beae1ea4845c6bab9314e4f84ac68742139d8c53" +checksum = "c1cc9717a20b1bb222f333e6a92fd32f7d8a18ddc5a3191a11af45dcbf4dcd16" dependencies = [ "autocfg", "scopeguard", @@ -628,18 +637,9 @@ dependencies = [ [[package]] name = "log" -version = "0.4.17" +version = "0.4.20" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "abb12e687cfb44aa40f41fc3978ef76448f9b6038cad6aef4259d3c095a2382e" -dependencies = [ - "cfg-if 1.0.0", -] - -[[package]] -name = 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dependencies = [ "libmimalloc-sys", ] [[package]] name = "miniz_oxide" -version = "0.5.3" +version = "0.7.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6f5c75688da582b8ffc1f1799e9db273f32133c49e048f614d22ec3256773ccc" +checksum = "e7810e0be55b428ada41041c41f32c9f1a42817901b4ccf45fa3d4b6561e74c7" dependencies = [ "adler", ] @@ -685,19 +685,19 @@ dependencies = [ [[package]] name = "num_cpus" -version = "1.13.1" +version = "1.16.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "19e64526ebdee182341572e50e9ad03965aa510cd94427a4549448f285e957a1" +checksum = "4161fcb6d602d4d2081af7c3a45852d875a03dd337a6bfdd6e06407b61342a43" dependencies = [ - "hermit-abi", + "hermit-abi 0.3.2", "libc", ] [[package]] name = "once_cell" -version = "1.13.0" +version = "1.18.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "18a6dbe30758c9f83eb00cbea4ac95966305f5a7772f3f42ebfc7fc7eddbd8e1" +checksum = 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"ee98ffd0b48ee95e6c5168188e44a54550b1564d9d530ee21d5f0eaed1069581" +dependencies = [ + "libc", + "zstd-sys", +] + +[[package]] +name = "zstd-sys" +version = "2.0.8+zstd.1.5.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5556e6ee25d32df2586c098bbfa278803692a20d0ab9565e049480d52707ec8c" +dependencies = [ + "cc", + "libc", + "pkg-config", +] diff --git a/Cargo.toml b/Cargo.toml index 9310764..dc767f9 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -31,6 +31,7 @@ bitvec = "1.0.1" bstr = "0.2.17" csv = "1.1.6" env_logger = "0.9.0" +fgoxide = { git = "https://github.com/kockan/fgoxide" } flate2 = {version = "1.0.22", default-features = false, features = ["zlib-ng-compat"]} flume = "0.10.9" gzp = "0.9.1" @@ -47,12 +48,14 @@ regex = "1.6.0" seq_io = "0.3.1" serde = {version = "1.0.130", features = ["derive"]} structopt = "0.3.23" +zstd = "0.12.4" [build-dependencies] built = {version ="0.5.1", features = ["git2"]} [dev-dependencies] -fgoxide = "0.1.3" +# Until fgoxide gets merged(?) to the original repo +fgoxide = { git = "https://github.com/kockan/fgoxide" } rstest = "0.12.0" seq_io = "0.3.1" tempfile = "3" diff --git a/rust-toolchain.toml b/rust-toolchain.toml index cc8f987..7f9aa4d 100644 --- a/rust-toolchain.toml +++ b/rust-toolchain.toml @@ -1,3 +1,3 @@ [toolchain] -channel = "1.64.0" +channel = "1.71.1" components = ["rustfmt", "clippy"] diff --git a/src/lib/mod.rs b/src/lib/mod.rs index aaaccfd..abe5606 100644 --- a/src/lib/mod.rs +++ b/src/lib/mod.rs @@ -8,7 +8,7 @@ pub mod color; pub mod matcher; use lazy_static::lazy_static; -use std::{borrow::Borrow, path::Path}; +use std::{borrow::Borrow}; pub const DNA_BASES: [u8; 5] = *b"ACGTN"; pub const IUPAC_BASES: [u8; 15] = *b"AGCTYRWSKMDVHBN"; @@ -44,33 +44,6 @@ where .collect() } -/// Returns true if the path ends with a recognized GZIP file extension -fn is_path_with_extension>(p: &P, extensions: [&str; 2]) -> bool { - if let Some(ext) = p.as_ref().extension() { - match ext.to_str() { - Some(x) => extensions.contains(&x), - None => false, - } - } else { - false - } -} - -/// The set of file extensions to treat as GZIPPED -const GZIP_EXTENSIONS: [&str; 2] = ["gz", "bgz"]; - -/// Returns true if the path ends with a recognized GZIP file extension -pub fn is_gzip_path>(p: &P) -> bool { - is_path_with_extension(p, GZIP_EXTENSIONS) -} - -/// The set of file extensions to treat as FASTQ -const FASTQ_EXTENSIONS: [&str; 2] = ["fastq", "fq"]; - -/// Returns true if the path ends with a recognized FASTQ file extension -pub fn is_fastq_path>(p: &P) -> bool { - is_path_with_extension(p, FASTQ_EXTENSIONS) -} // Tests #[cfg(test)] @@ -78,7 +51,6 @@ pub mod tests { use crate::*; use rstest::rstest; use std::str; - use tempfile::TempDir; // ############################################################################################ // Tests reverse_complement() @@ -92,33 +64,4 @@ pub mod tests { let string_result = str::from_utf8(&result).unwrap(); assert_eq!(&string_result, &expected); } - - // ############################################################################################ - // Tests is_gzip_path() - // ############################################################################################ - - #[rstest] - #[case("test_fastq.fq.gz", true)] // .fq.gz is valid gzip - #[case("test_fastq.fq.bgz", true)] // .fq.bgz is valid gzip - #[case("test_fastq.fq.tar", false)] // .fq.tar is invalid gzip - fn test_is_gzip_path(#[case] file_name: &str, #[case] expected: bool) { - let dir = TempDir::new().unwrap(); - let file_path = dir.path().join(file_name); - let result = is_gzip_path(&file_path); - assert_eq!(result, expected); - } - // ############################################################################################ - // Tests is_fastq_path() - // ############################################################################################ - - #[rstest] - #[case("test_fastq.fq", true)] // .fq is valid fastq - #[case("test_fastq.fastq", true)] // .fastq is valid fastq - #[case("test_fastq.sam", false)] // .sam is invalid fastq - fn test_is_fastq_path(#[case] file_name: &str, #[case] expected: bool) { - let dir = TempDir::new().unwrap(); - let file_path = dir.path().join(file_name); - let result = is_fastq_path(&file_path); - assert_eq!(result, expected); - } } diff --git a/src/main.rs b/src/main.rs index 2e9f833..ae4d046 100644 --- a/src/main.rs +++ b/src/main.rs @@ -5,8 +5,8 @@ use anyhow::{bail, ensure, Context, Result}; use env_logger::Env; use flate2::bufread::MultiGzDecoder; use flume::{bounded, Receiver, Sender}; +use fgoxide::io::Io; use fqgrep_lib::matcher::{validate_fixed_pattern, Matcher, MatcherFactory, MatcherOpts}; -use fqgrep_lib::{is_fastq_path, is_gzip_path}; use gzp::BUFSIZE; use isatty::stdout_isatty; use itertools::{self, izip, Itertools}; @@ -24,6 +24,7 @@ use std::{ }; use structopt::clap::arg_enum; use structopt::{clap::AppSettings, StructOpt}; +use zstd::stream::Decoder as ZstdDecoder; /// The number of reads in a chunk const CHUNKSIZE: usize = 5000; // * num_cpus::get(); @@ -127,7 +128,7 @@ impl FastqWriter { fn spawn_reader(file: PathBuf, decompress: bool) -> Receiver> { let (tx, rx) = bounded(READER_CHANNEL_SIZE); std::thread::spawn(move || { - // Open the file or standad input + // Open the file or standard input let raw_handle = if file.as_os_str() == "-" { Box::new(std::io::stdin()) as Box } else { @@ -140,9 +141,12 @@ fn spawn_reader(file: PathBuf, decompress: bool) -> Receiver> { let buf_handle = BufReader::with_capacity(BUFSIZE, raw_handle); // Maybe wrap it in a decompressor let maybe_decoder_handle = { - let is_gzip = is_gzip_path(&file) || (!is_fastq_path(&file) && decompress); + let is_gzip = Io::is_gzip_path(&file) || (!Io::is_fastq_path(&file) && decompress); + let is_zstd = Io::is_zstd_path(&file); if is_gzip { Box::new(MultiGzDecoder::new(buf_handle)) as Box + } else if is_zstd { + Box::new(ZstdDecoder::new(buf_handle).unwrap()) as Box } else { Box::new(buf_handle) as Box } @@ -562,7 +566,7 @@ pub mod tests { /// /// # Examples /// if - sequences = vec![vec!["AAGTCTGAATCCATGGAAAGCTATTG", "GGGTCTGAATCCATGGAAAGCTATTG"], vec!["AAGTCTGAATCCATGGAAAGCTATTG", "GGGTCTGAATCCATGGAAAGCTATTG"]] - /// write_fastq() will return Vec where 'paths' are Strings. + /// write_fastq() will return Vec where 'paths' are Strings. fn write_fastq( temp_dir: &TempDir, sequences_per_fastq: &Vec>, @@ -907,7 +911,7 @@ pub mod tests { } // ############################################################################################ - // Tests that correct match count is returned from .fq, .fastq, .fq.gz, and .fq.bgz + // Tests that correct match count is returned from .fq, .fastq, .fq.gz, .fq.bgz, and .fq.zst // ############################################################################################ // Three matches are found from all file types #[rstest] @@ -915,6 +919,7 @@ pub mod tests { #[case(String::from(".fastq"), 3)] #[case(String::from(".fq.gz"), 3)] #[case(String::from(".fq.bgz"), 3)] + #[case(String::from(".fq.zst"), 3)] fn test_fastq_compression(#[case] extension: String, #[case] expected: usize) { let dir = TempDir::new().unwrap(); let seqs = vec![