From 876755ea403731662cad0a3931e5f810d17c52a9 Mon Sep 17 00:00:00 2001 From: Rob Patro Date: Wed, 10 Jul 2024 12:02:46 -0400 Subject: [PATCH] more robust handling of paths --- Cargo.lock | 233 +++++++++++++++++++++-------------------- Cargo.toml | 2 +- src/main.rs | 2 +- src/piscem_commands.rs | 36 +++++-- 4 files changed, 149 insertions(+), 124 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 60d90cf..a9703b0 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -10,56 +10,57 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" [[package]] name = "aho-corasick" -version = "1.1.2" +version = "1.1.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0" +checksum = "8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916" dependencies = [ "memchr", ] [[package]] name = "anstream" -version = "0.6.12" +version = "0.6.14" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "96b09b5178381e0874812a9b157f7fe84982617e48f71f4e3235482775e5b540" +checksum = "418c75fa768af9c03be99d17643f93f79bbba589895012a80e3452a19ddda15b" dependencies = [ "anstyle", "anstyle-parse", "anstyle-query", "anstyle-wincon", "colorchoice", + "is_terminal_polyfill", "utf8parse", ] [[package]] name = "anstyle" -version = "1.0.6" +version = "1.0.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8901269c6307e8d93993578286ac0edf7f195079ffff5ebdeea6a59ffb7e36bc" +checksum = "038dfcf04a5feb68e9c60b21c9625a54c2c0616e79b72b0fd87075a056ae1d1b" [[package]] name = "anstyle-parse" -version = "0.2.3" +version = "0.2.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c" +checksum = "c03a11a9034d92058ceb6ee011ce58af4a9bf61491aa7e1e59ecd24bd40d22d4" dependencies = [ "utf8parse", ] [[package]] name = "anstyle-query" -version = "1.0.2" +version = "1.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e28923312444cdd728e4738b3f9c9cac739500909bb3d3c94b43551b16517648" +checksum = "ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391" dependencies = [ "windows-sys 0.52.0", ] [[package]] name = "anstyle-wincon" -version = "3.0.2" +version = "3.0.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7" +checksum = "61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19" dependencies = [ "anstyle", "windows-sys 0.52.0", @@ -73,9 +74,9 @@ checksum = "b3d1d046238990b9cf5bcde22a3fb3584ee5cf65fb2765f454ed428c7a0063da" [[package]] name = "bitflags" -version = "2.4.2" +version = "2.6.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ed570934406eb16438a4e976b1b4500774099c13b8cb96eec99f620f05090ddf" +checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de" [[package]] name = "block-buffer" @@ -88,19 +89,18 @@ dependencies = [ [[package]] name = "buffer-redux" -version = "1.0.0" +version = "1.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d2886ea01509598caac116942abd33ab5a88fa32acdf7e4abfa0fc489ca520c9" +checksum = "4c9f8ddd22e0a12391d1e7ada69ec3b0da1914f1cec39c5cf977143c5b2854f5" dependencies = [ "memchr", - "safemem", ] [[package]] name = "bytecount" -version = "0.6.7" +version = "0.6.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e1e5f035d16fc623ae5f74981db80a439803888314e3a555fd6f04acd51a3205" +checksum = "5ce89b21cab1437276d2650d57e971f9d548a2d9037cc231abdc0562b97498ce" [[package]] name = "bzip2" @@ -125,9 +125,9 @@ dependencies = [ [[package]] name = "cc" -version = "1.0.88" +version = "1.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "02f341c093d19155a6e41631ce5971aac4e9a868262212153124c15fa22d1cdc" +checksum = "eaff6f8ce506b9773fa786672d63fc7a191ffea1be33f72bbd4aeacefca9ffc8" [[package]] name = "cfg-if" @@ -172,9 +172,9 @@ dependencies = [ [[package]] name = "clap_lex" -version = "0.7.0" +version = "0.7.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "98cc8fbded0c607b7ba9dd60cd98df59af97e84d24e49c8557331cfc26d301ce" +checksum = "4b82cf0babdbd58558212896d1a4272303a57bdb245c2bf1147185fb45640e70" [[package]] name = "cmake" @@ -187,9 +187,9 @@ dependencies = [ [[package]] name = "colorchoice" -version = "1.0.0" +version = "1.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7" +checksum = "0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422" [[package]] name = "cpufeatures" @@ -202,9 +202,9 @@ dependencies = [ [[package]] name = "crc32fast" -version = "1.4.0" +version = "1.4.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b3855a8a784b474f333699ef2bbca9db2c4a1f6d9088a90a2d25b1eb53111eaa" +checksum = "a97769d94ddab943e4510d138150169a2758b5ef3eb191a9ee688de3e23ef7b3" dependencies = [ "cfg-if", ] @@ -231,9 +231,9 @@ dependencies = [ [[package]] name = "errno" -version = "0.3.8" +version = "0.3.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a258e46cdc063eb8519c00b9fc845fc47bcfca4130e2f08e88665ceda8474245" +checksum = "534c5cf6194dfab3db3242765c03bbe257cf92f22b38f6bc0c58d59108a820ba" dependencies = [ "libc", "windows-sys 0.52.0", @@ -241,9 +241,9 @@ dependencies = [ [[package]] name = "flate2" -version = "1.0.28" +version = "1.0.30" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e" +checksum = "5f54427cfd1c7829e2a139fcefea601bf088ebca651d2bf53ebc600eac295dae" dependencies = [ "crc32fast", "miniz_oxide", @@ -267,9 +267,9 @@ checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea" [[package]] name = "hermit-abi" -version = "0.3.8" +version = "0.3.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "379dada1584ad501b383485dd706b8afb7a70fcbc7f4da7d780638a5a6124a60" +checksum = "d231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024" [[package]] name = "hex" @@ -277,35 +277,41 @@ version = "0.4.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7f24254aa9a54b5c858eaee2f5bccdb46aaf0e486a595ed5fd8f86ba55232a70" +[[package]] +name = "is_terminal_polyfill" +version = "1.70.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f8478577c03552c21db0e2724ffb8986a5ce7af88107e6be5d2ee6e158c12800" + [[package]] name = "itoa" -version = "1.0.10" +version = "1.0.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b1a46d1a171d865aa5f83f92695765caa047a9b4cbae2cbf37dbd613a793fd4c" +checksum = "49f1f14873335454500d59611f1cf4a4b0f786f9ac11f4312a78e4cf2566695b" [[package]] name = "lazy_static" -version = "1.4.0" +version = "1.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646" +checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe" [[package]] name = "libc" -version = "0.2.153" +version = "0.2.155" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd" +checksum = "97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c" [[package]] name = "linux-raw-sys" -version = "0.4.13" +version = "0.4.14" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "01cda141df6706de531b6c46c3a33ecca755538219bd484262fa09410c13539c" +checksum = "78b3ae25bc7c8c38cec158d1f2757ee79e9b3740fbc7ccf0e59e4b08d793fa89" [[package]] name = "log" -version = "0.4.20" +version = "0.4.22" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b5e6163cb8c49088c2c36f57875e58ccd8c87c7427f7fbd50ea6710b2f3f2e8f" +checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24" [[package]] name = "lzma-sys" @@ -329,15 +335,15 @@ dependencies = [ [[package]] name = "memchr" -version = "2.7.1" +version = "2.7.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "523dc4f511e55ab87b694dc30d0f820d60906ef06413f93d4d7a1385599cc149" +checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3" [[package]] name = "miniz_oxide" -version = "0.7.2" +version = "0.7.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9d811f3e15f28568be3407c8e7fdb6514c1cda3cb30683f15b6a1a1dc4ea14a7" +checksum = "b8a240ddb74feaf34a79a7add65a741f3167852fba007066dcac1ca548d89c08" dependencies = [ "adler", ] @@ -390,13 +396,13 @@ checksum = "b15813163c1d831bf4a13c3610c05c0d03b39feb07f7e09fa234dac9b15aaf39" [[package]] name = "pin-project-lite" -version = "0.2.13" +version = "0.2.14" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8afb450f006bf6385ca15ef45d71d2288452bc3683ce2e2cacc0d18e4be60b58" +checksum = "bda66fc9667c18cb2758a2ac84d1167245054bcf85d5d1aaa6923f45801bdd02" [[package]] name = "piscem" -version = "0.10.1" +version = "0.10.2" dependencies = [ "anyhow", "clap", @@ -430,32 +436,32 @@ dependencies = [ [[package]] name = "proc-macro2" -version = "1.0.78" +version = "1.0.86" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e2422ad645d89c99f8f3e6b88a9fdeca7fabeac836b1002371c4367c8f984aae" +checksum = "5e719e8df665df0d1c8fbfd238015744736151d4445ec0836b8e628aae103b77" dependencies = [ "unicode-ident", ] [[package]] name = "quote" -version = "1.0.35" +version = "1.0.36" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "291ec9ab5efd934aaf503a6466c5d5251535d108ee747472c3977cc5acc868ef" +checksum = "0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7" dependencies = [ "proc-macro2", ] [[package]] name = "regex" -version = "1.10.3" +version = "1.10.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b62dbe01f0b06f9d8dc7d49e05a0785f153b00b2c227856282f671e0318c9b15" +checksum = "b91213439dad192326a0d7c6ee3955910425f441d7038e0d6933b0aec5c4517f" dependencies = [ "aho-corasick", "memchr", - "regex-automata 0.4.5", - "regex-syntax 0.8.2", + "regex-automata 0.4.7", + "regex-syntax 0.8.4", ] [[package]] @@ -469,13 +475,13 @@ dependencies = [ [[package]] name = "regex-automata" -version = "0.4.5" +version = "0.4.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5bb987efffd3c6d0d8f5f89510bb458559eab11e4f869acb20bf845e016259cd" +checksum = "38caf58cc5ef2fed281f89292ef23f6365465ed9a41b7a7754eb4e26496c92df" dependencies = [ "aho-corasick", "memchr", - "regex-syntax 0.8.2", + "regex-syntax 0.8.4", ] [[package]] @@ -486,15 +492,15 @@ checksum = "f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1" [[package]] name = "regex-syntax" -version = "0.8.2" +version = "0.8.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c08c74e62047bb2de4ff487b251e4a92e24f48745648451635cec7d591162d9f" +checksum = "7a66a03ae7c801facd77a29370b4faec201768915ac14a721ba36f20bc9c209b" [[package]] name = "rustix" -version = "0.38.31" +version = "0.38.34" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6ea3e1a662af26cd7a3ba09c0297a31af215563ecf42817c98df621387f4e949" +checksum = "70dc5ec042f7a43c4a73241207cecc9873a06d45debb38b329f8541d85c2730f" dependencies = [ "bitflags", "errno", @@ -505,30 +511,24 @@ dependencies = [ [[package]] name = "ryu" -version = "1.0.17" 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"e0cd7e117be63d3c3678776753929474f3b04a43a080c744d6b0ae2a8c28e222" dependencies = [ "proc-macro2", "quote", @@ -537,9 +537,9 @@ dependencies = [ [[package]] name = "serde_json" -version = "1.0.114" +version = "1.0.120" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c5f09b1bd632ef549eaa9f60a1f8de742bdbc698e6cee2095fc84dde5f549ae0" +checksum = "4e0d21c9a8cae1235ad58a00c11cb40d4b1e5c784f1ef2c537876ed6ffd8b7c5" dependencies = [ "itoa", "ryu", @@ -560,9 +560,9 @@ dependencies = [ [[package]] name = "sha2-asm" -version = "0.6.3" +version = "0.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f27ba7066011e3fb30d808b51affff34f0a66d3a03a58edd787c6e420e40e44e" +checksum = "b845214d6175804686b2bd482bcffe96651bb2d1200742b712003504a2dac1ab" dependencies = [ "cc", ] @@ -578,21 +578,21 @@ dependencies = [ [[package]] name = "smallvec" -version = "1.13.1" +version = "1.13.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e6ecd384b10a64542d77071bd64bd7b231f4ed5940fba55e98c3de13824cf3d7" +checksum = "3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67" [[package]] name = "strsim" -version = "0.11.0" +version = "0.11.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5ee073c9e4cd00e28217186dbe12796d692868f432bf2e97ee73bed0c56dfa01" +checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f" [[package]] name = "syn" -version = "2.0.51" +version = "2.0.70" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6ab617d94515e94ae53b8406c628598680aa0c9587474ecbe58188f7b345d66c" +checksum = "2f0209b68b3613b093e0ec905354eccaedcfe83b8cb37cbdeae64026c3064c16" dependencies = [ "proc-macro2", "quote", @@ -694,9 +694,9 @@ checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b" [[package]] name = "utf8parse" -version = "0.2.1" +version = "0.2.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a" +checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821" [[package]] name = "valuable" @@ -747,7 +747,7 @@ version = "0.52.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d" dependencies = [ - "windows-targets 0.52.3", + "windows-targets 0.52.6", ] [[package]] @@ -767,17 +767,18 @@ dependencies = [ [[package]] name = "windows-targets" -version = "0.52.3" +version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d380ba1dc7187569a8a9e91ed34b8ccfc33123bbacb8c0aed2d1ad7f3ef2dc5f" +checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973" dependencies = [ - "windows_aarch64_gnullvm 0.52.3", - "windows_aarch64_msvc 0.52.3", - "windows_i686_gnu 0.52.3", - "windows_i686_msvc 0.52.3", - "windows_x86_64_gnu 0.52.3", - "windows_x86_64_gnullvm 0.52.3", - "windows_x86_64_msvc 0.52.3", + "windows_aarch64_gnullvm 0.52.6", + "windows_aarch64_msvc 0.52.6", + "windows_i686_gnu 0.52.6", + "windows_i686_gnullvm", + "windows_i686_msvc 0.52.6", + "windows_x86_64_gnu 0.52.6", + "windows_x86_64_gnullvm 0.52.6", + "windows_x86_64_msvc 0.52.6", ] [[package]] @@ -788,9 +789,9 @@ checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8" [[package]] name = "windows_aarch64_gnullvm" -version = "0.52.3" +version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "68e5dcfb9413f53afd9c8f86e56a7b4d86d9a2fa26090ea2dc9e40fba56c6ec6" +checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3" [[package]] name = "windows_aarch64_msvc" @@ -800,9 +801,9 @@ checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc" [[package]] name = "windows_aarch64_msvc" -version = "0.52.3" +version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8dab469ebbc45798319e69eebf92308e541ce46760b49b18c6b3fe5e8965b30f" +checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469" [[package]] name = "windows_i686_gnu" @@ -812,9 +813,15 @@ checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e" [[package]] name = "windows_i686_gnu" -version = "0.52.3" +version = "0.52.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b" + +[[package]] +name = "windows_i686_gnullvm" +version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2a4e9b6a7cac734a8b4138a4e1044eac3404d8326b6c0f939276560687a033fb" +checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66" [[package]] name = "windows_i686_msvc" @@ -824,9 +831,9 @@ checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406" [[package]] name = "windows_i686_msvc" -version = "0.52.3" +version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "28b0ec9c422ca95ff34a78755cfa6ad4a51371da2a5ace67500cf7ca5f232c58" +checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66" [[package]] name = "windows_x86_64_gnu" @@ -836,9 +843,9 @@ checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e" [[package]] name = "windows_x86_64_gnu" -version = "0.52.3" +version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "704131571ba93e89d7cd43482277d6632589b18ecf4468f591fbae0a8b101614" +checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78" [[package]] name = "windows_x86_64_gnullvm" @@ -848,9 +855,9 @@ checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc" [[package]] name = "windows_x86_64_gnullvm" -version = "0.52.3" +version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "42079295511643151e98d61c38c0acc444e52dd42ab456f7ccfd5152e8ecf21c" +checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d" [[package]] name = "windows_x86_64_msvc" @@ -860,9 +867,9 @@ checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538" [[package]] name = "windows_x86_64_msvc" -version = "0.52.3" +version = "0.52.6" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0770833d60a970638e989b3fa9fd2bb1aaadcf88963d1659fd7d9990196ed2d6" +checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec" [[package]] name = "xz2" diff --git a/Cargo.toml b/Cargo.toml index 3e3c7f1..11ca634 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "piscem" -version = "0.10.1" +version = "0.10.2" edition = "2021" build = "build.rs" repository = "https://github.com/COMBINE-lab/piscem" diff --git a/src/main.rs b/src/main.rs index 9ab838a..898eb86 100644 --- a/src/main.rs +++ b/src/main.rs @@ -406,7 +406,7 @@ fn main() -> Result<(), anyhow::Error> { // about the references being indexed. } - info!("piscem build finished"); + info!("piscem build finished."); } Commands::MapSC(sc_opts) => { diff --git a/src/piscem_commands.rs b/src/piscem_commands.rs index aff084e..20dcbfe 100644 --- a/src/piscem_commands.rs +++ b/src/piscem_commands.rs @@ -132,7 +132,7 @@ pub(crate) struct MapSCOpts { #[arg(short, long)] pub geometry: String, - /// path to list of read 1 files + /// path to a ',' separated list of read 1 files #[arg( short = '1', long, @@ -142,7 +142,7 @@ pub(crate) struct MapSCOpts { )] pub read1: Vec, - /// path to list of read 2 files + /// path to a ',' separated list of read 2 files #[arg( short = '2', long, @@ -158,7 +158,7 @@ pub(crate) struct MapSCOpts { /// path to output directory #[arg(short, long)] - pub output: String, + pub output: PathBuf, /// do not consider poison k-mers, even if the underlying index contains them. /// In this case, the mapping results will be identical to those obtained as if @@ -218,7 +218,7 @@ pub(crate) struct MapBulkOpts { #[arg(short, long, help_heading = "Input")] pub index: String, - /// path to list of read 1 files + /// path to a comma-separated list of read 1 files #[arg( short = '1', long, @@ -228,7 +228,7 @@ pub(crate) struct MapBulkOpts { )] pub read1: Option>, - /// path to list of read 2 files + /// path to a ',' separated list of read 2 files #[arg( short = '2', long, @@ -238,7 +238,7 @@ pub(crate) struct MapBulkOpts { )] pub read2: Option>, - /// path to list of read unpaired read files + /// path to a ',' separated list of read unpaired read files #[arg(short = 'r', long, help_heading = "Input", value_delimiter = ',', conflicts_with_all = ["read1", "read2"])] pub reads: Option>, @@ -248,7 +248,7 @@ pub(crate) struct MapBulkOpts { /// path to output directory #[arg(short, long)] - pub output: String, + pub output: PathBuf, /// do not consider poison k-mers, even if the underlying index contains them. /// In this case, the mapping results will be identical to those obtained as if @@ -333,7 +333,16 @@ impl AsArgv for MapSCOpts { CString::new("-t").unwrap(), CString::new(self.threads.to_string()).unwrap(), CString::new("-o").unwrap(), - CString::new(self.output.as_str()).unwrap(), + #[cfg(not(target_os = "windows"))] + CString::new(std::os::unix::ffi::OsStrExt::as_bytes( + ::clone(&self.output) + .into_os_string() + .as_os_str(), + )) + .unwrap(), + // NOTE: Windows is completely untested + #[cfg(target_os = "windows")] + CString::new(self.output.into_os_string().to_str()?).unwrap(), ]; /*if self.list_geometries { @@ -411,7 +420,16 @@ impl AsArgv for MapBulkOpts { CString::new("-t").unwrap(), CString::new(self.threads.to_string()).unwrap(), CString::new("-o").unwrap(), - CString::new(self.output.as_str()).unwrap(), + #[cfg(not(target_os = "windows"))] + CString::new(std::os::unix::ffi::OsStrExt::as_bytes( + ::clone(&self.output) + .into_os_string() + .as_os_str(), + )) + .unwrap(), + // NOTE: Windows is completely untested + #[cfg(target_os = "windows")] + CString::new(self.output.into_os_string().to_str()?).unwrap(), ]; if let Some(ref unpaired_reads) = &self.reads {