diff --git a/Cargo.lock b/Cargo.lock index bd302e0..26619e3 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -10,9 +10,9 @@ checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" [[package]] name = "ahash" -version = "0.8.2" +version = "0.8.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bf6ccdb167abbf410dcb915cabd428929d7f6a04980b54a11f26a39f1c7f7107" +checksum = "2c99f64d1e06488f620f932677e24bc6e2897582980441ae90a671415bd7ec2f" dependencies = [ "cfg-if", "getrandom", @@ -22,23 +22,23 @@ dependencies = [ [[package]] name = "aho-corasick" -version = "0.7.19" +version = "1.0.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b4f55bd91a0978cbfd91c457a164bab8b4001c833b7f323132c0a4e1922dd44e" +checksum = "43f6cb1bf222025340178f382c426f13757b2960e89779dfcb319c32542a5a41" dependencies = [ "memchr", ] [[package]] name = "alevin-fry" -version = "0.9.0" +version = "0.8.2" dependencies = [ "ahash", "anyhow", "arrayvec", "bincode", "bio-types", - "bstr 1.1.0", + "bstr", "chrono", "clap", "crossbeam-channel", @@ -81,6 +81,12 @@ dependencies = [ "num-traits", ] +[[package]] +name = "android-tzdata" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0" + [[package]] name = "android_system_properties" version = "0.1.5" @@ -90,11 +96,60 @@ dependencies = [ "libc", ] +[[package]] +name = "anstream" +version = "0.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0ca84f3628370c59db74ee214b3263d58f9aadd9b4fe7e711fd87dc452b7f163" +dependencies = [ + "anstyle", + "anstyle-parse", + "anstyle-query", + "anstyle-wincon", + "colorchoice", + "is-terminal", + "utf8parse", +] + +[[package]] +name = "anstyle" +version = "1.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "3a30da5c5f2d5e72842e00bcb57657162cdabef0931f40e2deb9b4140440cecd" + +[[package]] +name = "anstyle-parse" +version = "0.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "938874ff5980b03a87c5524b3ae5b59cf99b1d6bc836848df7bc5ada9643c333" +dependencies = [ + "utf8parse", +] + +[[package]] +name = "anstyle-query" +version = "1.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5ca11d4be1bab0c8bc8734a9aa7bf4ee8316d462a08c6ac5052f888fef5b494b" +dependencies = [ + "windows-sys 0.48.0", +] + +[[package]] +name = "anstyle-wincon" +version = "1.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "180abfa45703aebe0093f79badacc01b8fd4ea2e35118747e5811127f926e188" +dependencies = [ + "anstyle", + "windows-sys 0.48.0", +] + [[package]] name = "anyhow" -version = "1.0.68" +version = "1.0.71" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2cb2f989d18dd141ab8ae82f64d1a8cdd37e0840f73a406896cf5e99502fab61" +checksum = "9c7d0618f0e0b7e8ff11427422b64564d5fb0be1940354bfe2e0529b18a9d9b8" [[package]] name = "approx" @@ -116,9 +171,9 @@ dependencies = [ [[package]] name = "arrayvec" -version = "0.7.2" +version = "0.7.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8da52d66c7071e2e3fa2a1e5c6d088fec47b593032b254f5e980de8ea54454d6" +checksum = "96d30a06541fbafbc7f82ed10c06164cfbd2c401138f6addd8404629c4b16711" [[package]] name = "atty" @@ -148,9 +203,9 @@ dependencies = [ [[package]] name = "bio-types" -version = "0.13.0" +version = "1.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dfa990f40a28735fa598dc3dd58d73e62e6b41458959d623903b927ba7b04c80" +checksum = "c915bf6c578d40e1e497f8c571a4514bc89c3195cec2abb8be6dd5500405c752" dependencies = [ "derive-new", "lazy_static", @@ -168,21 +223,9 @@ checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" [[package]] name = "bstr" -version = "0.2.17" +version = "1.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ba3569f383e8f1598449f1a423e72e99569137b47740b1da11ef19af3d5c3223" -dependencies = [ - "lazy_static", - "memchr", - "regex-automata", - "serde", -] - -[[package]] -name = "bstr" -version = "1.1.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b45ea9b00a7b3f2988e9a65ad3917e62123c38dba709b666506207be96d1790b" +checksum = "a246e68bb43f6cd9db24bea052a53e40405417c5fb372e3d1a8a7f770a564ef5" dependencies = [ "memchr", "once_cell", @@ -191,10 +234,10 @@ dependencies = [ ] [[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", @@ -202,9 +245,9 @@ dependencies = [ [[package]] name = "bumpalo" -version = "3.11.1" +version = "3.13.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "572f695136211188308f16ad2ca5c851a712c464060ae6974944458eb83880ba" +checksum = "a3e2c3daef883ecc1b5d58c15adae93470a91d425f3532ba1695849656af3fc1" [[package]] name = "bytecount" @@ -214,9 +257,9 @@ checksum = "2c676a478f63e9fa2dd5368a42f28bba0d6c560b775f38583c8bbaa7fcd67c9c" [[package]] name = "bytemuck" -version = "1.12.1" +version = "1.13.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2f5715e491b5a1598fc2bef5a606847b5dc1d48ea625bd3c02c00de8285591da" +checksum = "17febce684fd15d89027105661fec94afb475cb995fbc59d2865198446ba2eea" [[package]] name = "byteorder" @@ -226,9 +269,9 @@ checksum = "14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610" [[package]] name = "bzip2" -version = "0.4.3" +version = "0.4.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6afcd980b5f3a45017c57e57a2fcccbb351cc43a356ce117ef760ef8052b89b0" +checksum = "bdb116a6ef3f6c3698828873ad02c3014b3c85cadb88496095628e3ef1e347f8" dependencies = [ "bzip2-sys", "libc", @@ -247,9 +290,9 @@ dependencies = [ [[package]] name = "cc" -version = "1.0.78" +version = "1.0.79" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a20104e2335ce8a659d6dd92a51a767a0c062599c73b343fd152cb401e828c3d" +checksum = "50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f" dependencies = [ "jobserver", ] @@ -262,95 +305,96 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" [[package]] name = "chrono" -version = "0.4.23" +version = "0.4.26" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "16b0a3d9ed01224b22057780a37bb8c5dbfe1be8ba48678e7bf57ec4b385411f" +checksum = "ec837a71355b28f6556dbd569b37b3f363091c0bd4b2e735674521b4c5fd9bc5" dependencies = [ + "android-tzdata", "iana-time-zone", "js-sys", - "num-integer", "num-traits", - "time 0.1.44", + "time 0.1.45", "wasm-bindgen", "winapi", ] [[package]] name = "clap" -version = "4.0.32" +version = "4.3.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a7db700bc935f9e43e88d00b0850dae18a63773cfbec6d8e070fccf7fef89a39" +checksum = "bba77a07e4489fb41bd90e8d4201c3eb246b3c2c9ea2ba0bddd6c1d1df87db7d" dependencies = [ - "bitflags", + "clap_builder", "clap_derive", + "once_cell", +] + +[[package]] +name = "clap_builder" +version = "4.3.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2c9b4a88bb4bc35d3d6f65a21b0f0bafe9c894fa00978de242c555ec28bea1c0" +dependencies = [ + "anstream", + "anstyle", + "bitflags", "clap_lex", - "is-terminal", "once_cell", "strsim", - "termcolor", - "terminal_size 0.2.3", + "terminal_size", ] [[package]] name = "clap_derive" -version = "4.0.21" +version = "4.3.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0177313f9f02afc995627906bbd8967e2be069f5261954222dac78290c2b9014" +checksum = "b8cd2b2a819ad6eec39e8f1d6b53001af1e5469f8c177579cdaeb313115b825f" dependencies = [ "heck", - "proc-macro-error", "proc-macro2", "quote", - "syn", + "syn 2.0.22", ] [[package]] name = "clap_lex" -version = "0.3.0" +version = "0.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0d4198f73e42b4936b35b5bb248d81d2b595ecb170da0bac7655c54eedfa8da8" -dependencies = [ - "os_str_bytes", -] +checksum = "2da6da31387c7e4ef160ffab6d5e7f00c42626fe39aea70a7b0f1773f7dd6c1b" [[package]] name = "cmake" -version = "0.1.49" +version = "0.1.50" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "db34956e100b30725f2eb215f90d4871051239535632f84fea3bc92722c66b7c" +checksum = "a31c789563b815f77f4250caee12365734369f942439b7defd71e18a48197130" dependencies = [ "cc", ] [[package]] -name = "codespan-reporting" -version = "0.11.1" +name = "colorchoice" +version = "1.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3538270d33cc669650c4b093848450d380def10c331d38c768e34cac80576e6e" -dependencies = [ - "termcolor", - "unicode-width", -] +checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7" [[package]] name = "console" -version = "0.15.2" +version = "0.15.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c050367d967ced717c04b65d8c619d863ef9292ce0c5760028655a2fb298718c" +checksum = "c926e00cc70edefdc64d3a5ff31cc65bb97a3460097762bd23afb4d8145fccf8" dependencies = [ "encode_unicode", "lazy_static", "libc", - "terminal_size 0.1.17", "unicode-width", - "winapi", + "windows-sys 0.45.0", ] [[package]] name = "core-foundation-sys" -version = "0.8.3" +version = "0.8.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5827cebf4670468b8772dd191856768aedcb1b0278a04f989f7766351917b9dc" +checksum = "e496a50fda8aacccc86d7529e2c1e0892dbd0f898a6b5645b5561b89c3210efa" [[package]] name = "crc32fast" @@ -363,9 +407,9 @@ dependencies = [ [[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", "crossbeam-utils", @@ -373,9 +417,9 @@ 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", "crossbeam-epoch", @@ -384,9 +428,9 @@ dependencies = [ [[package]] name = "crossbeam-epoch" -version = "0.9.11" +version = "0.9.15" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f916dfc5d356b0ed9dae65f1db9fc9770aa2851d2662b988ccf4fe3516e86348" +checksum = "ae211234986c545741a7dc064309f67ee1e5ad243d0e48335adc0484d960bcc7" dependencies = [ "autocfg", "cfg-if", @@ -407,22 +451,21 @@ dependencies = [ [[package]] name = "crossbeam-utils" -version = "0.8.12" +version = "0.8.16" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "edbafec5fa1f196ca66527c1b12c2ec4745ca14b50f1ad8f9f6f720b55d11fac" +checksum = "5a22b2d63d4d1dc0b7f1b6b2747dd0088008a9be28b6ddf0b1e7d335e3037294" dependencies = [ "cfg-if", ] [[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 0.2.17", "csv-core", - "itoa 0.4.8", + "itoa", "ryu", "serde", ] @@ -442,50 +485,6 @@ version = "0.1.7" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9" -[[package]] -name = "cxx" -version = "1.0.81" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "97abf9f0eca9e52b7f81b945524e76710e6cb2366aead23b7d4fbf72e281f888" -dependencies = [ - "cc", - "cxxbridge-flags", - "cxxbridge-macro", - "link-cplusplus", -] - -[[package]] -name = "cxx-build" -version = "1.0.81" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7cc32cc5fea1d894b77d269ddb9f192110069a8a9c1f1d441195fba90553dea3" -dependencies = [ - "cc", - "codespan-reporting", - "once_cell", - "proc-macro2", - "quote", - "scratch", - "syn", -] - -[[package]] -name = "cxxbridge-flags" -version = "1.0.81" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = 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source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a9c384f161156f5260c24a097c56119f9be8c798586aecc13afbcbe7b7e26bf8" +checksum = "a62bc1cf6f830c2ec14a513a9fb124d0a213a629668a4186f329db21fe045652" dependencies = [ "percent-encoding", ] @@ -600,9 +599,9 @@ dependencies = [ [[package]] name = "getrandom" -version = "0.2.8" +version = "0.2.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c05aeb6a22b8f62540c194aac980f2115af067bfe15a0734d7277a768d396b31" +checksum = "be4136b2a15dd319360be1c07d9933517ccf0be8f16bf62a3bee4f0d618df427" dependencies = [ "cfg-if", "libc", @@ -611,9 +610,9 @@ dependencies = [ [[package]] name = "glob" -version = "0.3.0" +version = "0.3.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9b919933a397b79c37e33b77bb2aa3dc8eb6e165ad809e58ff75bc7db2e34574" +checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b" [[package]] name = "hashbrown" @@ -623,9 +622,9 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+ "num-complex 0.4.3", "num-integer", "num-traits", "rawpointer", @@ -976,11 +965,11 @@ dependencies = [ [[package]] name = "needletail" -version = "0.4.1" +version = "0.5.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7fb4c43ebd04b0e776119c8fc3bd4c28178619cd04e1f19f600a4ef0282fa3cc" +checksum = "db05a5ab397f64070d8c998fa0fbb84e484b81f95752af317dac183a82d9295d" dependencies = [ - "buf_redux", + "buffer-redux", "bytecount", "bzip2", "flate2", @@ -1004,7 +993,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "43db66d1170d347f9a065114077f7dccb00c1b9478c89384490a3425279a4606" dependencies = [ "num-bigint", - "num-complex 0.4.2", + "num-complex 0.4.3", "num-integer", "num-iter", "num-rational", @@ -1034,9 +1023,9 @@ dependencies = [ [[package]] name = "num-complex" -version = "0.4.2" +version = "0.4.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = 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"/libradicl/src/*.rs", "/src/*.rs", "/Cargo.toml", "/README.md", @@ -38,48 +37,48 @@ categories = ["command-line-utilities", "science"] [dependencies] # for local development, look in the libradicl git repository # but when published, pull the specified version -libradicl = { git = "https://github.com/COMBINE-lab/libradicl", version = "0.5.1" } -anyhow = "1.0.68" -arrayvec = "0.7.2" -ahash = "0.8.2" +libradicl = { git = "https://github.com/COMBINE-lab/libradicl", branch = "develop", version = "0.6.0" } +anyhow = "1.0.71" +arrayvec = "0.7.4" +ahash = "0.8.3" bincode = "1.3.3" -bstr = "1.1.0" -crossbeam-channel = "0.5.6" +bstr = "1.5.0" +crossbeam-channel = "0.5.8" crossbeam-queue = "0.3.8" # derive_builder = "0.11.2" -typed-builder = "0.11.0" -indicatif = "0.17.2" -needletail = "0.4.1" -petgraph = "0.6.2" -flate2 = "1.0.25" +typed-builder = "0.14.0" +indicatif = "0.17.5" +needletail = "0.5.1" +petgraph = "0.6.3" +flate2 = "1.0.26" scroll = "0.11.0" -serde = { version = "1.0.152", features = ["derive"] } -serde_json = "1.0.91" -sprs = "0.11.0" +serde = { version = "1.0.164", features = ["derive"] } +serde_json = "1.0.99" +sprs = "0.11.1" slog = "2.7.0" slog-term = "2.9.0" slog-async = "2.7.0" smallvec = "1.10.0" snap = "1.1.0" rand = "0.8.5" -chrono = "0.4.23" -csv = "1.1.6" -mimalloc = { version = "0.1.34", default-features = false } +chrono = "0.4.26" +csv = "1.2.2" +mimalloc = { version = "0.1.37", default-features = false } num-format = "0.4.4" -num_cpus = "1.15.0" -bio-types = { version = "0.13.0", default-features = true, features = ["serde"] } -itertools = "0.10.5" -thiserror = "1.0.38" +num_cpus = "1.16.0" +bio-types = { version = "1.0.0", default-features = true, features = ["serde"] } +itertools = "0.11.0" +thiserror = "1.0.40" statrs = "0.16.0" -rust-htslib = { version = "0.40.2", default-features = false, features = [ +rust-htslib = { version = "0.44.1", default-features = false, features = [ "bzip2", "lzma", ] } -sce = { git = "https://github.com/parazodiac/SingleCellExperiment", version = "0.1.2" } +sce = { git = "https://github.com/parazodiac/SingleCellExperiment", branch = "dev", version = "0.2.0" } # no shenanigans; clap makes breaking "fixes" too often to allow variability # in the version different from what we tested with -clap = { version = "=4.0.32", features = ["derive", "wrap_help", "cargo", "help", "usage", "string", "error-context"] } +clap = { version = "=4.3.9", features = ["derive", "wrap_help", "cargo", "help", "usage", "string", "error-context"] } [profile.release] #debug = true diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst index 9d93ff0..8bfdd24 100644 --- a/docs/source/getting_started.rst +++ b/docs/source/getting_started.rst @@ -4,7 +4,7 @@ Getting Started Running the alevin-fry pipeline ------------------------------- -First, we need to generate a RAD file using alevin. The RAD file is created by mapping the sequencing reads against an index of the reference. We recommend using a `splici `_ reference index. The mappings can be generated using either `selective-alignemnt `_ or `pseudoalignemnt `_ against the transcriptiome (with the ``--rad`` or ``--sketch`` flags, respectively). **Note**, however, that alevin-fry does not currently support RAD files aligned against a decoy-aware index, so that indices used for RAD file generation should be prepared without decoy sequnece. For a chromium v2 set of read files, the command would look like the following: +First, we need to generate a RAD file using alevin. The RAD file is created by mapping the sequencing reads against an index of the reference. We recommend using a `splici `_ reference index. The mappings can be generated using either `selective-alignment `_ or `pseudoalignment `_ against the transcriptome (with the ``--rad`` or ``--sketch`` flags, respectively). **Note**, however, that alevin-fry does not currently support RAD files aligned against a decoy-aware index, so that indices used for RAD file generation should be prepared without decoy sequnece. For a chromium v2 set of read files, the command would look like the following: .. code:: bash diff --git a/src/collate.rs b/src/collate.rs index 68bcafa..40be896 100644 --- a/src/collate.rs +++ b/src/collate.rs @@ -24,7 +24,7 @@ use serde_json::json; use std::collections::HashMap; use std::fs::File; use std::io::BufReader; -use std::io::{BufWriter, Cursor, Read, Seek, SeekFrom, Write}; +use std::io::{BufWriter, Cursor, Read, Seek, Write}; use std::iter::FromIterator; use std::path::{Path, PathBuf}; use std::str::FromStr; @@ -369,8 +369,7 @@ where // the exact position at the end of the header, // precisely sizeof(u64) bytes beyond the num_chunks field. - let end_header_pos = - br.get_ref().seek(SeekFrom::Current(0)).unwrap() - (br.buffer().len() as u64); + let end_header_pos = br.get_ref().stream_position().unwrap() - (br.buffer().len() as u64); info!( log, @@ -398,7 +397,7 @@ where let umit = rl_tags.tags[1].typeid; // the exact position at the end of the header + file tags - let pos = br.get_ref().seek(SeekFrom::Current(0)).unwrap() - (br.buffer().len() as u64); + let pos = br.get_ref().stream_position().unwrap() - (br.buffer().len() as u64); // copy the header { diff --git a/src/convert.rs b/src/convert.rs index 8ec4fdd..47fe434 100644 --- a/src/convert.rs +++ b/src/convert.rs @@ -166,8 +166,7 @@ where } // keep a pointer to header pos - let end_header_pos = - data.seek(SeekFrom::Current(0)).unwrap() - std::mem::size_of::() as u64; + let end_header_pos = data.stream_position().unwrap() - std::mem::size_of::() as u64; // check header position info!(log, "end header pos: {:?}", end_header_pos,); diff --git a/src/infer.rs b/src/infer.rs index 43bad7c..abd70ec 100644 --- a/src/infer.rs +++ b/src/infer.rs @@ -53,8 +53,8 @@ pub fn infer( .unwrap_or_else(|| panic!("cannot get parent path of {:?}", count_mat_path)); // read the file and convert it to csr (rows are *cells*) - let count_mat: sprs::CsMatBase, Vec, Vec, _> = - match sprs::io::read_matrix_market::(count_mat_path) { + let count_mat: sprs::CsMatBase, Vec, Vec, _> = + match sprs::io::read_matrix_market::(count_mat_path) { Ok(t) => t.to_csr(), Err(e) => { warn!(log, "error reading mtx file{:?}", e); @@ -359,7 +359,11 @@ pub fn infer( // gather the data from the row's iterator into a vector of // (eq_id, count) tuples. - let cell_data: Vec<(u32, u32)> = row_vec.iter().map(|e| (e.0 as u32, *e.1)).collect(); + // NOTE: because of the matrix market format requirements (and the compatible + // implmentation in sprs), we have read the matrix in with i32 instead of u32 entries. + // Here we convert the i32 counts (the second element of the tuple here) to u32. + let cell_data: Vec<(u32, u32)> = + row_vec.iter().map(|e| (e.0 as u32, *e.1 as u32)).collect(); // keep pushing this data onto our work queue while we can. // launch off these cells on the queue let mut cd_clone = (processed_ind, cell_data.clone()); diff --git a/src/quant.rs b/src/quant.rs index f1954a9..835dd4f 100644 --- a/src/quant.rs +++ b/src/quant.rs @@ -47,18 +47,13 @@ use libradicl::rad_types; type BufferedGzFile = BufWriter>; -#[derive(PartialEq, Eq, Debug, Clone, Copy, Serialize)] +#[derive(PartialEq, Eq, Debug, Default, Clone, Copy, Serialize)] pub enum SplicedAmbiguityModel { PreferAmbiguity, + #[default] WinnerTakeAll, } -impl Default for SplicedAmbiguityModel { - fn default() -> Self { - SplicedAmbiguityModel::WinnerTakeAll - } -} - // Implement the trait impl FromStr for SplicedAmbiguityModel { type Err = &'static str; @@ -71,9 +66,10 @@ impl FromStr for SplicedAmbiguityModel { } } -#[derive(PartialEq, Eq, Debug, Clone, Copy, Serialize)] +#[derive(PartialEq, Eq, Debug, Default, Clone, Copy, Serialize)] pub enum ResolutionStrategy { Trivial, + #[default] CellRangerLike, CellRangerLikeEm, ParsimonyEm, @@ -82,12 +78,6 @@ pub enum ResolutionStrategy { ParsimonyGene, } -impl Default for ResolutionStrategy { - fn default() -> Self { - ResolutionStrategy::CellRangerLike - } -} - impl fmt::Display for ResolutionStrategy { fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result { write!(f, "{:?}", self)