diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..7a751c2 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "skani-mummer-train"] + path = skani-mummer-train + url = https://github.com/bluenote-1577/skani-mummer-train diff --git a/Cargo.lock b/Cargo.lock index 97e9e68..7acbbff 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -57,6 +57,15 @@ dependencies = [ "winapi", ] +[[package]] +name = "autocfg" +version = "0.1.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0dde43e75fd43e8a1bf86103336bc699aa8d17ad1be60c76c0bdfd4828e19b78" +dependencies = [ + "autocfg 1.1.0", +] + [[package]] name = "autocfg" version = "1.1.0" @@ -99,7 +108,7 @@ dependencies = [ "num-traits", "ordered-float", "petgraph", - "rand", + "rand 0.8.5", "regex", "serde", "serde_derive", @@ -151,19 +160,6 @@ version = "1.3.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" -[[package]] -name = "boomphf" -version = "0.5.9" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4e8fb7f38fef59c32549861151d63a6190865e60cf690340c13e3d7178b42a2f" -dependencies = [ - "crossbeam-utils", - "log", - "rayon", - "serde", - "wyhash", -] - [[package]] name = "bstr" version = "0.2.17" @@ -241,6 +237,12 @@ version = "1.0.74" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "581f5dba903aac52ea3feb5ec4810848460ee833876f1f9b0fdeab1f19091574" +[[package]] +name = "cfg-if" +version = "0.1.10" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4785bdd1c96b2a846b2bd7cc02e86b6b3dbf14e7e53446c4f54c92a361040822" + [[package]] name = "cfg-if" version = "1.0.0" @@ -271,13 +273,22 @@ dependencies = [ "os_str_bytes", ] +[[package]] +name = "cloudabi" +version = "0.0.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ddfc5b9aa5d4507acaf872de71051dfd0e309860e88966e1051e462a077aac4f" +dependencies = [ + "bitflags", +] + [[package]] name = "crc32fast" version = "1.3.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "b540bd8bc810d3885c6ea91e2018302f68baba2129ab3e88f32389ee9370880d" dependencies = [ - "cfg-if", + "cfg-if 1.0.0", ] [[package]] @@ -286,7 +297,7 @@ version = "0.5.6" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "c2dd04ddaf88237dc3b8d8f9a3c1004b506b54b3313403944054d23c0870c521" dependencies = [ - "cfg-if", + "cfg-if 1.0.0", "crossbeam-utils", ] @@ -296,7 +307,7 @@ version = "0.8.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "715e8152b692bba2d374b53d4875445368fdf21a94751410af607a5ac677d1fc" dependencies = [ - "cfg-if", + "cfg-if 1.0.0", "crossbeam-epoch", "crossbeam-utils", ] @@ -307,8 +318,8 @@ version = "0.9.11" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f916dfc5d356b0ed9dae65f1db9fc9770aa2851d2662b988ccf4fe3516e86348" dependencies = [ - "autocfg", - "cfg-if", + "autocfg 1.1.0", + "cfg-if 1.0.0", "crossbeam-utils", "memoffset", "scopeguard", @@ -320,7 +331,7 @@ version = "0.8.12" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "edbafec5fa1f196ca66527c1b12c2ec4745ca14b50f1ad8f9f6f720b55d11fac" dependencies = [ - "cfg-if", + "cfg-if 1.0.0", ] [[package]] @@ -357,30 +368,13 @@ version = "5.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "907076dfda823b0b36d2a1bb5f90c96660a5bbcd7729e10727f07858f22c4edc" dependencies = [ - "cfg-if", + "cfg-if 1.0.0", "hashbrown", "lock_api", "once_cell", "parking_lot_core", ] -[[package]] -name = "debruijn" -version = "0.3.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "346d29ff45270b3642817082a513e55765ef5686b68e6cc0ed595897a64439d5" -dependencies = [ - "bit-set", - "boomphf", - "itertools", - "log", - "num-traits", - "serde", - "serde_derive", - "serde_json", - "smallvec", -] - [[package]] name = "derive-new" version = "0.5.9" @@ -482,6 +476,12 @@ version = "1.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "2022715d62ab30faffd124d40b76f4134a550a87792276512b18d63272333394" +[[package]] +name = "fuchsia-cprng" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a06f77d526c1a601b7c4cdd98f54b5eaabffc14d5f2f0296febdc7f357c6d3ba" + [[package]] name = "futures" version = "0.3.25" @@ -568,6 +568,20 @@ dependencies = [ "byteorder", ] +[[package]] +name = "gbdt" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "74248386ea349f903cee13fae53f41bdae987f74eb798c6cbcb08370c99ccd34" +dependencies = [ + "cfg-if 0.1.10", + "rand 0.6.5", + "regex", + "serde", + "serde_derive", + "serde_json", +] + [[package]] name = "gcollections" version = "1.5.0" @@ -586,7 +600,7 @@ version = "0.2.8" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "c05aeb6a22b8f62540c194aac980f2115af067bfe15a0734d7277a768d396b31" dependencies = [ - "cfg-if", + "cfg-if 1.0.0", "libc", "wasi", ] @@ -630,7 +644,7 @@ version = "1.9.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "10a35a97730320ffe8e2d410b5d3b69279b98d2c14bdb8b70ea89ecf7888d41e" dependencies = [ - "autocfg", + "autocfg 1.1.0", "hashbrown", ] @@ -640,7 +654,7 @@ version = "0.1.12" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c" dependencies = [ - "cfg-if", + "cfg-if 1.0.0", ] [[package]] @@ -710,7 +724,7 @@ version = "0.4.9" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "435011366fe56583b16cf956f9df0095b405b82d76425bc8981c0e22e60ec4df" dependencies = [ - "autocfg", + "autocfg 1.1.0", "scopeguard", ] @@ -720,7 +734,7 @@ version = "0.4.17" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "abb12e687cfb44aa40f41fc3978ef76448f9b6038cad6aef4259d3c095a2382e" dependencies = [ - "cfg-if", + "cfg-if 1.0.0", ] [[package]] @@ -755,7 +769,7 @@ version = "0.6.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5aa361d4faea93603064a027415f07bd8e1d5c88c9fbf68bf56a285428fd79ce" dependencies = [ - "autocfg", + "autocfg 1.1.0", ] [[package]] @@ -788,7 +802,7 @@ dependencies = [ "num-complex", "num-rational", "num-traits", - "rand", + "rand 0.8.5", "rand_distr", "simba", "typenum", @@ -841,12 +855,6 @@ dependencies = [ "rustc_version", ] -[[package]] -name = "nohash-hasher" -version = "0.2.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2bf50223579dc7cdcfb3bfcacf7069ff68243f8c363f62ffa99cf000a6b9c451" - [[package]] name = "normalize-line-endings" version = "0.3.0" @@ -868,7 +876,7 @@ version = "0.1.45" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9" dependencies = [ - "autocfg", + "autocfg 1.1.0", "num-traits", ] @@ -878,7 +886,7 @@ version = "0.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0638a1c9d0a3c0914158145bc76cff373a75a627e6ecbfb71cbe6f453a5a19b0" dependencies = [ - "autocfg", + "autocfg 1.1.0", "num-integer", "num-traits", ] @@ -889,7 +897,7 @@ version = "0.2.15" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd" dependencies = [ - "autocfg", + "autocfg 1.1.0", "libm", ] @@ -940,7 +948,7 @@ version = "0.9.5" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7ff9f3fef3968a3ec5945535ed654cb38ff72d7495a25619e2247fb15a2ed9ba" dependencies = [ - "cfg-if", + "cfg-if 1.0.0", "libc", "redox_syscall 0.2.16", "smallvec", @@ -1079,6 +1087,25 @@ dependencies = [ "proc-macro2", ] +[[package]] +name = "rand" +version = "0.6.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6d71dacdc3c88c1fde3885a3be3fbab9f35724e6ce99467f7d9c5026132184ca" +dependencies = [ + "autocfg 0.1.8", + "libc", + "rand_chacha 0.1.1", + "rand_core 0.4.2", + "rand_hc", + "rand_isaac", + "rand_jitter", + "rand_os", + "rand_pcg", + "rand_xorshift", + "winapi", +] + [[package]] name = "rand" version = "0.8.5" @@ -1086,8 +1113,18 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404" dependencies = [ "libc", - "rand_chacha", - "rand_core", + "rand_chacha 0.3.1", + "rand_core 0.6.4", +] + +[[package]] +name = "rand_chacha" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "556d3a1ca6600bfcbab7c7c91ccb085ac7fbbcd70e008a98742e7847f4f7bcef" +dependencies = [ + "autocfg 0.1.8", + "rand_core 0.3.1", ] [[package]] @@ -1097,9 +1134,24 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88" dependencies = [ "ppv-lite86", - "rand_core", + "rand_core 0.6.4", +] + +[[package]] +name = "rand_core" +version = "0.3.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7a6fdeb83b075e8266dcc8762c22776f6877a63111121f5f8c7411e5be7eed4b" +dependencies = [ + "rand_core 0.4.2", ] +[[package]] +name = "rand_core" +version = "0.4.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9c33a3c44ca05fa6f1807d8e6743f3824e8509beca625669633be0acbdf509dc" + [[package]] name = "rand_core" version = "0.6.4" @@ -1116,7 +1168,69 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "32cb0b9bc82b0a0876c2dd994a7e7a2683d3e7390ca40e6886785ef0c7e3ee31" dependencies = [ "num-traits", - "rand", + "rand 0.8.5", +] + +[[package]] +name = "rand_hc" +version = "0.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7b40677c7be09ae76218dc623efbf7b18e34bced3f38883af07bb75630a21bc4" +dependencies = [ + "rand_core 0.3.1", +] + +[[package]] +name = "rand_isaac" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ded997c9d5f13925be2a6fd7e66bf1872597f759fd9dd93513dd7e92e5a5ee08" +dependencies = [ + "rand_core 0.3.1", +] + +[[package]] +name = "rand_jitter" +version = "0.1.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1166d5c91dc97b88d1decc3285bb0a99ed84b05cfd0bc2341bdf2d43fc41e39b" +dependencies = [ + "libc", + "rand_core 0.4.2", + "winapi", +] + +[[package]] +name = "rand_os" +version = "0.1.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7b75f676a1e053fc562eafbb47838d67c84801e38fc1ba459e8f180deabd5071" +dependencies = [ + "cloudabi", + "fuchsia-cprng", + "libc", + "rand_core 0.4.2", + "rdrand", + "winapi", +] + +[[package]] +name = "rand_pcg" +version = "0.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "abf9b09b01790cfe0364f52bf32995ea3c39f4d2dd011eac241d2914146d0b44" +dependencies = [ + "autocfg 0.1.8", + "rand_core 0.4.2", +] + +[[package]] +name = "rand_xorshift" +version = "0.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "cbf7e9e623549b0e21f6e97cf8ecf247c1a8fd2e8a992ae265314300b2455d5c" +dependencies = [ + "rand_core 0.3.1", ] [[package]] @@ -1131,7 +1245,7 @@ version = "1.5.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "bd99e5772ead8baa5215278c9b15bf92087709e9c1b2d1f97cdb5a183c933a7d" dependencies = [ - "autocfg", + "autocfg 1.1.0", "crossbeam-deque", "either", "rayon-core", @@ -1149,6 +1263,15 @@ dependencies = [ "num_cpus", ] +[[package]] +name = "rdrand" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "678054eb77286b51581ba43620cc911abf02758c91f93f479767aed0f90458b2" +dependencies = [ + "rand_core 0.3.1", +] + [[package]] name = "redox_syscall" version = "0.1.57" @@ -1327,27 +1450,27 @@ dependencies = [ [[package]] name = "skani" -version = "0.0.1" +version = "0.1.0" dependencies = [ "assert_cmd", "bincode", "bio", "clap", - "debruijn", "fastrand", "fxhash", + "gbdt", "gcollections", "intervallum", "log", "needletail", - "nohash-hasher", "num-traits", "partitions", "predicates 1.0.8", - "rand", + "rand 0.8.5", "rayon", "rust-lapper", "serde", + "serde_json", "serial_test", "simple-logging", "smallvec", @@ -1362,7 +1485,7 @@ version = "0.4.7" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "4614a76b2a8be0058caa9dbbaf66d988527d86d003c11a94fbd335d7661edcef" dependencies = [ - "autocfg", + "autocfg 1.1.0", ] [[package]] @@ -1384,7 +1507,7 @@ dependencies = [ "lazy_static", "nalgebra", "num-traits", - "rand", + "rand 0.8.5", ] [[package]] @@ -1648,15 +1771,6 @@ version = "0.42.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f40009d85759725a34da6d89a94e63d7bdc50a862acf0dbc7c8e488f1edcb6f5" -[[package]] -name = "wyhash" -version = "0.5.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "baf6e163c25e3fac820b4b453185ea2dea3b6a3e0a721d4d23d75bd33734c295" -dependencies = [ - "rand_core", -] - [[package]] name = "xz2" version = "0.1.7" diff --git a/Cargo.toml b/Cargo.toml index d937fc5..f09b435 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "skani" -version = "0.0.1" +version = "0.1.0" edition = "2021" license = "MIT OR Apache-2.0" @@ -12,23 +12,25 @@ bio = "*" rand = "0.8.3" fxhash = "*" clap = "3" -debruijn = "*" partitions = "*" num-traits = "*" needletail = "*" simple-logging= "*" log = "*" rayon = "*" -nohash-hasher = "*" smallvec = { version = "*", features = ["union","serde","write"] } serde = "*" bincode = "*" intervallum = "*" rust-lapper = "*" gcollections = "*" +fastrand="*" +gbdt = "*" +serde_json = "*" statrs = "*" + +[target.'cfg(target_env = "x86_64")'.dependencies] tikv-jemallocator = "*" -fastrand="*" [dev-dependencies] assert_cmd = "1.0.1" diff --git a/README.md b/README.md index 9d22b96..9dae449 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,25 @@ skani uses an approximate mapping method without base-level alignment to get ort 3. **Fast computations**. Indexing/sketching is ~ 3x faster than Mash, and querying is about 25x faster than FastANI (but slower than Mash). -4. **Efficient database search**. Querying a genome against a preprocessed database of >65000 prokaryotic genomes takes a few seconds with a single processor and ~5 GB of RAM. Constructing a database from genome sequences takes a few minutes to an hour. +4. **Efficient database search**. Querying a genome against a preprocessed database of >65000 prokaryotic genomes takes a few seconds with a single processor and ~6 GB of RAM. Constructing a database from genome sequences takes a few minutes to an hour. + +## Updates + +### v0.1.0 released - 2023-02-07. + +We added new experiments on the revised version of our preprint (pending bioRxiv update) in the appendix. We show skani has quite good AF correlation with MUMmer, and that it works decently on simple eukaryotic MAGs, especially with the `--slow` option (see below). + +#### Major + +* **ANI debiasing added** - skani now uses a debiasing step with a regression model trained on MAGs to give more accurate ANIs. v0.0.1 gave robust, but slightly overestimated ANIs, especially around 95-97% range. Debiasing is enabled by default, but can be turned off with ``--no-learned-ani``. +* **More accurate aligned fraction** - chaining algorithm changed to give a more accurate aligned fraction (AF) estimate. The previous version had more variance and underestimated AF for certain assemblies. + +#### Minor + +* **Small contig/genome defaults made better** - should be more sensitive so that they don't get filtered by default. +* **Repetitive k-mer masking made better** - smarter settings and should work better for eukaryotic genomes; shouldn't affect prokaryotic genomes much. +* **`--fast` and `--slow` mode added** - alias for `-c 200` and `-c 30` respectively. +* **More x86_64 builds should work** - there was a bug before where skani would be dysfunctional on non x86_64 architectures. It seems to at least build on ARM64 architectures successfully now. ## Install @@ -38,8 +56,6 @@ skani dist refs/e.coli-EC590.fasta refs/e.coli-K12.fasta #./target/release/skani dist refs/e.coli-EC590.fasta refs/e.coli-K12.fasta ``` -Note: If you're on an ARM64 platform, you may need to build from the `no-simd` branch of skani. See the issue [here](https://github.com/bluenote-1577/skani/issues/6). - #### Option 2: Pre-built x86-64 linux statically compiled executable We offer a pre-built statically compiled executable for x86-64 linux systems. That is, if you're on a x86-64 linux system, you can just download the binary and run it without installing anything. @@ -57,22 +73,16 @@ Note: the binary is compiled with a different set of libraries (musl instead of See the [Releases](https://github.com/bluenote-1577/skani/releases) page for obtaining specific versions of skani. -#### Option 3: Conda +#### Option 3: Conda (conda version: 0.0.1 - source version: 0.1.0) ```sh conda install -c bioconda skani ``` -Note: _I highly recommend options 1 and 2 over using conda right now_. skani is being developed quickly, and bugs are being fixed almost daily. The conda version will always be outdated. I'll remove this message when I feel skani is more stable. +Note: _I highly recommend options 1 and 2 over using conda right now_. skani is being developed quickly. The conda version will always be outdated. I'll remove this message when I feel skani is more stable. ## Quick start -### [skani commands usage information](https://github.com/bluenote-1577/skani/wiki/skani-basic-usage-guide) - -For more information about using the specific skani subcommands, see the [guide linked above](https://github.com/bluenote-1577/skani/wiki/skani-basic-usage-guide). - -All skani modes take the argument `-t` as number of threads (default: 3). - ```sh # compare two genomes for ANI. # all options take -t for multi-threading. @@ -99,6 +109,10 @@ python scripts/clustermap_triangle.py skani_ani_matrix.txt ## Tutorials and manuals +### [skani basic usage information](https://github.com/bluenote-1577/skani/wiki/skani-basic-usage-guide) + +For more information about using the specific skani subcommands, see the [guide linked above](https://github.com/bluenote-1577/skani/wiki/skani-basic-usage-guide). + ### skani tutorials 1. #### [Tutorial: setting up a 65000 prokaryotic genome database to search against](https://github.com/bluenote-1577/skani/wiki/Tutorial:-setting-up-a-65000-genome-database-to-search-against) diff --git a/model_to_src.sh b/model_to_src.sh new file mode 100755 index 0000000..d16a866 --- /dev/null +++ b/model_to_src.sh @@ -0,0 +1,17 @@ +#Models used in the preprint of skani. Trained on only Nayfach et al (2021) GEM data. +MODEL=./skani-mummer-train/v0.1.0-paper-models/0.19525746-3-195-0.06.model +MODEL_C200=./skani-mummer-train/v0.1.0-paper-models/0.19861849-3-195-0.089999996.model +SRC=src/model.rs + +echo $MODEL +echo $MODEL_C200 + +echo 'pub const MODEL:&str = r#"' > $SRC +cat $MODEL >> $SRC +echo '"#;' >> $SRC +printf '\n' >> $SRC + +echo 'pub const MODEL_C200:&str = r#"' >> $SRC +cat $MODEL_C200 >> $SRC +echo '"#;' >> $SRC +printf '\n' >> $SRC diff --git a/skani-mummer-train b/skani-mummer-train new file mode 160000 index 0000000..31057cd --- /dev/null +++ b/skani-mummer-train @@ -0,0 +1 @@ +Subproject commit 31057cda1983738c478866ea7e010c0e52dc6609 diff --git a/src/avx2_seeding.rs b/src/avx2_seeding.rs new file mode 100644 index 0000000..2439372 --- /dev/null +++ b/src/avx2_seeding.rs @@ -0,0 +1,260 @@ +use smallvec::SmallVec; +use std::arch::x86_64::*; +use crate::params::*; +use crate::types::*; + +#[inline] +#[target_feature(enable = "avx2")] +pub unsafe fn mm_hash256(kmer: __m256i) -> __m256i { + let mut key = kmer; + let s1 = _mm256_slli_epi64(key, 21); + key = _mm256_add_epi64(key, s1); + key = _mm256_xor_si256(key, _mm256_cmpeq_epi64(key, key)); + + key = _mm256_xor_si256(key, _mm256_srli_epi64(key, 24)); + let s2 = _mm256_slli_epi64(key, 3); + let s3 = _mm256_slli_epi64(key, 8); + + key = _mm256_add_epi64(key, s2); + key = _mm256_add_epi64(key, s3); + key = _mm256_xor_si256(key, _mm256_srli_epi64(key, 14)); + let s4 = _mm256_slli_epi64(key, 2); + let s5 = _mm256_slli_epi64(key, 4); + key = _mm256_add_epi64(key, s4); + key = _mm256_add_epi64(key, s5); + key = _mm256_xor_si256(key, _mm256_srli_epi64(key, 28)); + + let s6 = _mm256_slli_epi64(key, 31); + key = _mm256_add_epi64(key, s6); + + key +} + +#[target_feature(enable = "avx2")] +pub unsafe fn avx2_fmh_seeds( + string: &[u8], + sketch_params: &SketchParams, + contig_index: ContigIndex, + new_sketch: &mut Sketch, + seed: bool, +) { + if seed && new_sketch.kmer_seeds_k.is_none() { + new_sketch.kmer_seeds_k = Some(KmerSeeds::default()); + } + let marker_k = K_MARKER_DNA; + let kmer_seeds_k = &mut new_sketch.kmer_seeds_k; + let marker_seeds = &mut new_sketch.marker_seeds; + let k = sketch_params.k; + let c = sketch_params.c; + let marker_c = sketch_params.marker_c; + let len = (string.len() - marker_k + 1) / 4; + let string1 = &string[0..len + marker_k - 1]; + let string2 = &string[len..2 * len + marker_k - 1]; + let string3 = &string[2 * len..3 * len + marker_k - 1]; + let string4 = &string[3 * len..4 * len + marker_k - 1]; + if k > marker_k { + panic!("Value of k > {} for DNA; not allowed.", marker_k); + } + if string.len() < 2 * marker_k { + return; + } + + let mut rolling_kmer_f_marker = _mm256_set_epi64x(0, 0, 0, 0); + let mut rolling_kmer_r_marker = _mm256_set_epi64x(0, 0, 0, 0); + let rev_sub = _mm256_set_epi64x(3, 3, 3, 3); + for i in 0..marker_k - 1 { + let nuc_f1 = BYTE_TO_SEQ[string1[i] as usize] as i64; + let nuc_f2 = BYTE_TO_SEQ[string2[i] as usize] as i64; + let nuc_f3 = BYTE_TO_SEQ[string3[i] as usize] as i64; + let nuc_f4 = BYTE_TO_SEQ[string4[i] as usize] as i64; + let f_nucs = _mm256_set_epi64x(nuc_f4, nuc_f3, nuc_f2, nuc_f1); + let r_nucs = _mm256_sub_epi64(rev_sub, f_nucs); + + rolling_kmer_f_marker = _mm256_slli_epi64(rolling_kmer_f_marker, 2); + rolling_kmer_f_marker = _mm256_or_si256(rolling_kmer_f_marker, f_nucs); + + rolling_kmer_r_marker = _mm256_srli_epi64(rolling_kmer_r_marker, 2); + let shift_nuc_r = _mm256_slli_epi64(r_nucs, 40); + rolling_kmer_r_marker = _mm256_or_si256(rolling_kmer_r_marker, shift_nuc_r); + } + + let seed_mask = (MarkerBits::MAX >> (std::mem::size_of::() * 8 - 2 * k)) as i64; + let mm256_seed_mask = _mm256_set_epi64x(seed_mask, seed_mask, seed_mask, seed_mask); + let marker_mask = + (MarkerBits::MAX >> (std::mem::size_of::() * 8 - 2 * marker_k)) as i64; + let rev_marker_mask: u64 = !(3 << (2 * marker_k - 2)); + let rev_marker_mask = i64::from_le_bytes(rev_marker_mask.to_le_bytes()); + // dbg!(u64::MAX / (c as u64)); + // dbg!((u64::MAX / (c as u64)) as i64); + let threshold = i64::MIN + (u64::MAX / (c as u64)) as i64; + let _threshold_marker = i64::MIN + (u64::MAX / marker_c as u64) as i64; + let threshold_unsigned = u64::MAX / c as u64; + let threshold_marker_unsigned = u64::MAX / marker_c as u64; + let _cmp_thresh = _mm256_set_epi64x(threshold, threshold, threshold, threshold); + + let mm256_marker_mask = _mm256_set_epi64x(marker_mask, marker_mask, marker_mask, marker_mask); + let mm256_rev_marker_mask = _mm256_set_epi64x( + rev_marker_mask, + rev_marker_mask, + rev_marker_mask, + rev_marker_mask, + ); + + //dbg!(KmerEnc::print_string(u64::from_le_bytes(_mm256_extract_epi64(rolling_kmer_f_marker,0).to_le_bytes()), 21)); + + for i in marker_k-1..(len + marker_k - 1) { + let nuc_f1 = BYTE_TO_SEQ[string1[i] as usize] as i64; + let nuc_f2 = BYTE_TO_SEQ[string2[i] as usize] as i64; + let nuc_f3 = BYTE_TO_SEQ[string3[i] as usize] as i64; + let nuc_f4 = BYTE_TO_SEQ[string4[i] as usize] as i64; + let f_nucs = _mm256_set_epi64x(nuc_f4, nuc_f3, nuc_f2, nuc_f1); + let r_nucs = _mm256_sub_epi64(rev_sub, f_nucs); + + rolling_kmer_f_marker = _mm256_slli_epi64(rolling_kmer_f_marker, 2); + rolling_kmer_f_marker = _mm256_or_si256(rolling_kmer_f_marker, f_nucs); + rolling_kmer_f_marker = _mm256_and_si256(rolling_kmer_f_marker, mm256_marker_mask); + rolling_kmer_r_marker = _mm256_srli_epi64(rolling_kmer_r_marker, 2); + let shift_nuc_r = _mm256_slli_epi64(r_nucs, 40); + rolling_kmer_r_marker = _mm256_and_si256(rolling_kmer_r_marker, mm256_rev_marker_mask); + rolling_kmer_r_marker = _mm256_or_si256(rolling_kmer_r_marker, shift_nuc_r); + + let rolling_kmer_f_seed = _mm256_and_si256(rolling_kmer_f_marker, mm256_seed_mask); + let rolling_kmer_r_seed = _mm256_and_si256(rolling_kmer_r_marker, mm256_seed_mask); + let compare = _mm256_cmpgt_epi64(rolling_kmer_r_seed, rolling_kmer_f_seed); + let compare_marker = _mm256_cmpgt_epi64(rolling_kmer_r_marker, rolling_kmer_f_marker); + let canonical_seeds_256 = + _mm256_blendv_epi8(rolling_kmer_r_seed, rolling_kmer_f_seed, compare); + + let canonical = [ + _mm256_extract_epi64(compare, 0) != 0, + _mm256_extract_epi64(compare, 1) != 0, + _mm256_extract_epi64(compare, 2) != 0, + _mm256_extract_epi64(compare, 3) != 0, + ]; + + let canonical_seeds = [ + _mm256_extract_epi64(canonical_seeds_256, 0), + _mm256_extract_epi64(canonical_seeds_256, 1), + _mm256_extract_epi64(canonical_seeds_256, 2), + _mm256_extract_epi64(canonical_seeds_256, 3), + ]; + + let hash_256 = mm_hash256(canonical_seeds_256); + let v1 = _mm256_extract_epi64(hash_256, 0) as u64; + let v2 = _mm256_extract_epi64(hash_256, 1) as u64; + let v3 = _mm256_extract_epi64(hash_256, 2) as u64; + let v4 = _mm256_extract_epi64(hash_256, 3) as u64; + // let threshold_256 = _mm256_cmpgt_epi64(cmp_thresh, hash_256); + // let m1 = _mm256_extract_epi64(threshold_256, 0); + // let m2 = _mm256_extract_epi64(threshold_256, 1); + // let m3 = _mm256_extract_epi64(threshold_256, 2); + // let m4 = _mm256_extract_epi64(threshold_256, 3); + + if true { + // if m1 !={ + if v1 < threshold_unsigned { + const IND: i32 = 0; + let kmer_seeds = &mut kmer_seeds_k.as_mut().unwrap(); + let kmer_positions = kmer_seeds + .entry(canonical_seeds[IND as usize] as SeedBits) + .or_insert(SmallVec::<[SeedPosition; SMALL_VEC_SIZE]>::new()); + // .or_insert(vec![]); + kmer_positions.push(SeedPosition { + pos: i as GnPosition, + canonical: canonical[IND as usize], + contig_index, + phase: 0, + }); + let canonical_marker = _mm256_extract_epi64(compare_marker, IND) != 0; + let canonical_kmer_marker; + if canonical_marker { + canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_f_marker, IND); + } else { + canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_r_marker, IND); + }; + // if _mm256_extract_epi64(hash_256, IND) < threshold_marker { + if v1 < threshold_marker_unsigned { + marker_seeds.insert(canonical_kmer_marker as u64); + } + } + // if m2 != 0 { + if v2 < threshold_unsigned { + const IND: i32 = 1; + let kmer_seeds = &mut kmer_seeds_k.as_mut().unwrap(); + let kmer_positions = kmer_seeds + .entry(canonical_seeds[IND as usize] as SeedBits) + .or_insert(SmallVec::<[SeedPosition; SMALL_VEC_SIZE]>::new()); + // .or_insert(vec![]); + kmer_positions.push(SeedPosition { + pos: i as GnPosition + (len as i32 * IND) as GnPosition, + canonical: canonical[IND as usize], + contig_index, + phase: 0, + }); + let canonical_marker = _mm256_extract_epi64(compare_marker, IND) != 0; + let canonical_kmer_marker; + if canonical_marker { + canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_f_marker, IND); + } else { + canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_r_marker, IND); + }; + // if _mm256_extract_epi64(hash_256, IND) < threshold_marker { + if v2 < threshold_marker_unsigned { + marker_seeds.insert(canonical_kmer_marker as u64); + } + } + // if m3 != 0 { + if v3 < threshold_unsigned { + const IND: i32 = 2; + let kmer_seeds = &mut kmer_seeds_k.as_mut().unwrap(); + let kmer_positions = kmer_seeds + .entry(canonical_seeds[IND as usize] as SeedBits) + .or_insert(SmallVec::<[SeedPosition; SMALL_VEC_SIZE]>::new()); + // .or_insert(vec![]); + kmer_positions.push(SeedPosition { + canonical: canonical[IND as usize], + pos: i as GnPosition + (len as i32 * IND) as GnPosition, + contig_index, + phase: 0, + }); + let canonical_marker = _mm256_extract_epi64(compare_marker, IND) != 0; + let canonical_kmer_marker; + if canonical_marker { + canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_f_marker, IND); + } else { + canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_r_marker, IND); + }; + // if _mm256_extract_epi64(hash_256, IND) < threshold_marker { + if v3 < threshold_marker_unsigned { + marker_seeds.insert(canonical_kmer_marker as u64); + } + } + // if m4 != 0 { + if v4 < threshold_unsigned { + const IND: i32 = 3; + let kmer_seeds = &mut kmer_seeds_k.as_mut().unwrap(); + let kmer_positions = kmer_seeds + .entry(canonical_seeds[IND as usize] as SeedBits) + .or_insert(SmallVec::<[SeedPosition; SMALL_VEC_SIZE]>::new()); + // .or_insert(vec![]); + kmer_positions.push(SeedPosition { + pos: i as GnPosition + (len as i32 * IND) as GnPosition, + canonical: canonical[IND as usize], + contig_index, + phase: 0, + }); + let canonical_marker = _mm256_extract_epi64(compare_marker, IND) != 0; + let canonical_kmer_marker; + if canonical_marker { + canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_f_marker, IND); + } else { + canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_r_marker, IND); + }; + // if _mm256_extract_epi64(hash_256, IND) < threshold_marker { + if v4 < threshold_marker_unsigned { + marker_seeds.insert(canonical_kmer_marker as u64); + } + } + } + } +} diff --git a/src/chain.rs b/src/chain.rs index 9f3d115..4fcc531 100644 --- a/src/chain.rs +++ b/src/chain.rs @@ -6,7 +6,6 @@ use fxhash::FxHashMap; use log::*; use partitions::*; use std::mem; -use std::time::Instant; extern crate interval; use gcollections::ops::set::*; use interval::interval_set::*; @@ -36,14 +35,45 @@ fn switch_qr(med_ctg_len_r: f64, med_ctg_len_q: f64, q_sk_len: f64,r_sk_len: f64 // } } -fn bootstrap_interval(ani_ests: &Vec<(f64,usize)>) -> (f64,f64){ +fn mean(data: &[f64]) -> Option { + let sum = data.iter().sum::() as f64; + let count = data.len() as f64; + if data.len() > 0{ + return Some(sum/count); + } + else{ + return None; + } +} + +fn std_deviation(data: &[f64]) -> f64 { + let count = data.len(); + let data_mean = mean(&data); + if data_mean.is_none(){ + return 0. + } + else{ + let data_mean = data_mean.unwrap(); + let variance = data.iter().map(|value| { + let diff = data_mean - (*value); + + diff * diff + }).sum::() / count as f64; + + variance.sqrt() + } +} + +fn bootstrap_interval(ani_ests: &Vec<(f64,usize)>) -> (f64,f64,f64){ + let ani_est_no_mult = ani_ests.iter().map(|x| x.0).collect::>(); + let std = std_deviation(&ani_est_no_mult); let mut res = vec![]; let mut mult_ani_ests = vec![]; fastrand::seed(7); let num_samp = ani_ests.len(); //Return no confidence interval if number of samples is too small. if num_samp < 10 { - return (0.,1.); + return (0.,1., std); } for (ani,mult) in ani_ests.iter(){ for _ in 0..*mult{ @@ -61,7 +91,7 @@ fn bootstrap_interval(ani_ests: &Vec<(f64,usize)>) -> (f64,f64){ res.push(sum/(num_samp as f64)); } res.sort_by(|x,y| x.partial_cmp(y).unwrap()); - (res[iters * 5 / 100 - 1],res[iters * 95 / 100 - 1]) + (res[iters * 5 / 100 - 1],res[iters * 95 / 100 - 1], std) } @@ -76,7 +106,6 @@ pub fn map_params_from_sketch( let min_length_cover = if amino_acid{MIN_LENGTH_COVER_AAI} else {MIN_LENGTH_COVER}; let fragment_length = fragment_length_formula(ref_sketch.total_sequence_length, amino_acid); let length_cutoff = fragment_length; - trace!("Fragment length is {}.", fragment_length); let mut frac_cover_cutoff = command_params.min_aligned_frac; if frac_cover_cutoff < 0.{ if amino_acid { @@ -87,7 +116,7 @@ pub fn map_params_from_sketch( } let length_cover_cutoff = 5000000; let bp_chain_band = if amino_acid {BP_CHAIN_BAND_AAI} else {BP_CHAIN_BAND}; - let chain_band = bp_chain_band/ref_sketch.c; + let index_chain_band = bp_chain_band/ref_sketch.c; let min_score = min_anchors as f64 * anchor_score * 0.75; // let min_score = 0.; let k = ref_sketch.k; @@ -99,7 +128,7 @@ pub fn map_params_from_sketch( length_cutoff, frac_cover_cutoff, length_cover_cutoff, - chain_band, + index_chain_band, k, amino_acid, min_score, @@ -115,10 +144,7 @@ pub fn chain_seeds( query_sketch: &Sketch, map_params: MapParams, ) -> AniEstResult { - let now = Instant::now(); let (anchor_chunks, switched) = get_anchors(ref_sketch, query_sketch, &map_params); - debug!("Get anchors time: {}", now.elapsed().as_secs_f32()); - let now = Instant::now(); let chain_results = chain_anchors_ani(&anchor_chunks, &map_params); let mut good_intervals = vec![]; for i in 0..anchor_chunks.chunks.len() { @@ -126,10 +152,8 @@ pub fn chain_seeds( let anchors = &anchor_chunks.chunks[i]; get_chain_intervals(&mut good_intervals, chain_result, anchors, &map_params, i); } - debug!("Chain time: {}", now.elapsed().as_secs_f32()); let good_interval_chunks = get_nonoverlapping_chains(&mut good_intervals, anchor_chunks.chunks.len()); - let now = Instant::now(); let ani = calculate_ani( &good_interval_chunks, ref_sketch, @@ -138,7 +162,6 @@ pub fn chain_seeds( &map_params, switched, ); - debug!("Ani calc time: {}", now.elapsed().as_secs_f32()); ani } @@ -153,12 +176,21 @@ fn calculate_ani( let k = map_params.k; let mut ani_ests = vec![]; let c = ref_sketch.c as GnPosition; + let sensitive_af; + if c < 200{ + sensitive_af = true; + } + else{ + sensitive_af = false; + } let mut _num_good_chunks = 0; let mut _all_anchors_total = 0; let mut total_query_bases = 0; let mut total_ref_range = 0; let mut leftmost_interval = &ChainInterval::default(); let mut rightmost_interval = &ChainInterval::default(); + let mut avg_chain_int_len = 0; + let mut num_chains = 0; for (i, intervals) in int_chunks.iter().enumerate() { let mut all_intervals = vec![].to_interval_set(); let mut total_anchors = 0; @@ -204,20 +236,27 @@ fn calculate_ani( let stop = int.interval_on_query.1 + c; all_intervals = all_intervals.union(&vec![(start, stop)].to_interval_set()); //interval_vec.insert(int_insert, i); + if sensitive_af{ + total_query_bases += int.query_range_len() - int.overlap + 2 * c + k as GnPosition; + total_ref_range += int.query_range_len() - int.overlap + 2 * c + k as GnPosition; + } + + avg_chain_int_len += int.query_range_len() - int.overlap + 2 * c + k as GnPosition; + num_chains += 1; } if total_anchors == 0{ continue; } - if total_range_query.1 - total_range_query.0 < map_params.min_length_cover as GnPosition{ - total_query_bases += total_range_query.1 - total_range_query.0; - total_ref_range += total_range_query.1 - total_range_query.0; + if total_range_query.1 - total_range_query.0 < map_params.min_length_cover as GnPosition{ continue; } - total_query_bases += total_range_query.1 - total_range_query.0 + 2 * c + map_params.k as GnPosition; - total_ref_range += total_range_query.1 - total_range_query.0 + 2 * c + map_params.k as GnPosition; + if !sensitive_af{ + total_query_bases += total_range_query.1 - total_range_query.0 + 2 * c + map_params.k as GnPosition; + total_ref_range += total_range_query.1 - total_range_query.0 + 2 * c + map_params.k as GnPosition; + } let mut num_seeds_in_intervals = 0; let mut upper_lower_seeds = 0; @@ -230,18 +269,26 @@ fn calculate_ani( let mut left_spacing_est = 0; let mut right_spacing_est = 0; let switched_ref_sketch; + let switched_query_sketch; if switched{ + switched_query_sketch = &ref_sketch; switched_ref_sketch = &query_sketch; } else{ switched_ref_sketch = &ref_sketch; + switched_query_sketch = &query_sketch; } + let ref_ctg_len = switched_ref_sketch.contig_lengths[leftmost_interval.ref_contig]; + trace!("switched ref ctg len {},id {}", ref_ctg_len, leftmost_interval.ref_contig); + let q_ctg_len = switched_query_sketch.contig_lengths[leftmost_interval.query_contig]; + trace!("switched query ctg len {},id {}", q_ctg_len, leftmost_interval.query_contig); + + //TODO this was for testing... don't use this mechanism let extend = 0; if leftmost_interval.reverse_chain{ let ref_ctg_len =switched_ref_sketch.contig_lengths[leftmost_interval.ref_contig]; - trace!("{},{}", ref_ctg_len, leftmost_interval.ref_contig); if ref_ctg_len - leftmost_interval.interval_on_ref.1 < extend{ left_spacing_est = ref_ctg_len - leftmost_interval.interval_on_ref.1; } @@ -344,11 +391,11 @@ fn calculate_ani( } // ani_ests.push((ani_est, upper_lower_seeds)); trace!( - "Ani est fragment {}, total range {:?}, total anchors {}, seeds in fragment {:?}", + "Ani est fragment {}, total range {:?}, total anchors {}, seeds in fragment {:?},", ani_est, total_range_query, total_anchors, - anchor_chunks.seeds_in_chunk[i].len() + anchor_chunks.seeds_in_chunk[i].len(), ); trace!( "Intervals {:?}, Num Anchors in Interval {}, Total Anchors {}", @@ -361,11 +408,12 @@ fn calculate_ani( } ani_ests.sort_by(|x, y| x.partial_cmp(y).unwrap()); - if ani_ests.is_empty() { + if ani_ests.is_empty() || num_chains == 0 { let mut ret = AniEstResult::default(); ret.ani = f32::NAN; return ret; } + avg_chain_int_len /= num_chains; let mut total_multiplicitiy = 0; for ani in ani_ests.iter(){ total_multiplicitiy += ani.1; @@ -418,7 +466,9 @@ fn calculate_ani( let mut final_ani = weighted_avg / total_multiplicitiy as f64; // let (upper, lower) = z_interval(&ani_ests); - let ci = bootstrap_interval(&ani_ests); + let ci_std = bootstrap_interval(&ani_ests); + let ci = (ci_std.0, ci_std.1); + let std = ci_std.2; let covered_query = f64::min( 1., total_query_bases as f64 / query_sketch.total_sequence_length as f64, @@ -430,15 +480,16 @@ fn calculate_ani( let q_string = &query_sketch.file_name; let id_string = if map_params.amino_acid { "AAI" } else { "ANI" }; + debug!("Total 1-to-1 aligned bases: {}", total_query_bases); + //println!("{}",total_query_bases); debug!( - "Query {} Ref {} - {} {}, +/- = {}/{}. Covered {}", + "Query {} Ref {} - {} {}, +/- = {}/{}. ", q_string, ref_sketch.file_name, id_string, final_ani, ci.0, ci.1, - covered_query, ); if map_params.amino_acid{ @@ -451,6 +502,20 @@ fn calculate_ani( { final_ani = -1.; } + + let mut sorted_contigs_q = query_sketch.contig_lengths.clone(); + let mut sorted_contigs_r = ref_sketch.contig_lengths.clone(); + sorted_contigs_q.sort(); + sorted_contigs_r.sort(); + let qs_lens = sorted_contigs_q.len(); + let rs_lens = sorted_contigs_r.len(); + let contig_quants_q = [sorted_contigs_q[qs_lens * 10 / 100 ], sorted_contigs_q[qs_lens* 50 / 100], sorted_contigs_q[qs_lens * 90 / 100]]; + let contig_quants_r = [sorted_contigs_r[rs_lens * 10 / 100 ], sorted_contigs_r[rs_lens* 50 / 100], sorted_contigs_r[rs_lens * 90 / 100]]; +// let mean_contig_len_q = query_sketch.contig_lengths.iter().map(|x| *x as f64).sum::() +// /(query_sketch.contig_lengths.len() as f64); +// let mean_contig_len_r = ref_sketch.contig_lengths.iter().map(|x| *x as f64).sum::() +// /(ref_sketch.contig_lengths.len() as f64); + AniEstResult { ani: final_ani as f32, align_fraction_query: covered_query as f32, @@ -459,9 +524,20 @@ fn calculate_ani( query_file: query_sketch.file_name.clone(), query_contig: query_sketch.contigs[0].clone(), ref_contig: ref_sketch.contigs[0].clone(), + num_contigs_r: ref_sketch.contigs.len() as u32, + num_contigs_q: query_sketch.contigs.len() as u32, ci_upper: ci.1 as f32, ci_lower: ci.0 as f32, - aai: map_params.amino_acid + aai: map_params.amino_acid, + quant_90_contig_len_q: contig_quants_q[2] as f32, + quant_90_contig_len_r: contig_quants_r[2] as f32, + quant_50_contig_len_q: contig_quants_q[1] as f32, + quant_50_contig_len_r: contig_quants_r[1] as f32, + quant_10_contig_len_q: contig_quants_q[0] as f32, + quant_10_contig_len_r: contig_quants_r[0] as f32, + std: std as f32, + avg_chain_int_len, + total_bases_covered: total_query_bases, } } @@ -516,7 +592,7 @@ pub fn check_markers_quickly( query_sketch: &Sketch, screen_val: f64 ) -> bool{ - if screen_val <= 0.00{ + if screen_val <= 0.50 || ref_sketch.marker_seeds.len() == 0 || query_sketch.marker_seeds.len() == 0{ return true; } let seeds1; @@ -605,7 +681,7 @@ fn get_anchors( let mut anchors = vec![]; let mut query_kmers_with_hits = 0; for (canon_kmer, query_pos) in kmer_seeds_query.iter() { - if query_pos.len() > query_sketch.repetitive_kmers { + if query_pos.len() > map_params.index_chain_band{ continue; } let contains = kmer_seeds_ref.contains_key(canon_kmer); @@ -617,7 +693,7 @@ fn get_anchors( } else { let ref_pos = &kmer_seeds_ref[canon_kmer]; - if ref_pos.len() > ref_sketch.repetitive_kmers { + if ref_pos.len() > map_params.index_chain_band{ continue; } @@ -651,7 +727,7 @@ fn get_anchors( query_position_vec.sort_unstable(); } debug!( - "Ref seeds len {}, Query seeds len {}, Anchors {}, Seeds hit query {}, Est {}", + "Ref seeds len {}, Query seeds len {}, Anchors {}, Seeds hit query {}, Est {}, Ref_file {}, Query_file {}", kmer_seeds_ref.len(), kmer_seeds_query.len(), anchors.len(), @@ -660,6 +736,8 @@ fn get_anchors( (query_kmers_with_hits as f64) / (kmer_seeds_query.len() as f64), 1. / (k as f64) ), + ref_sketch.file_name, + query_sketch.file_name, ); let mut lengths = vec![]; let mut chunks = vec![]; @@ -783,7 +861,7 @@ fn chain_anchors_ani(anchor_chunks: &AnchorChunks, map_params: &MapParams) -> Ve continue; } if anchor_curr.query_pos - anchor_past.query_pos > past_chain_length - || i - j > map_params.chain_band + || i - j > map_params.index_chain_band { break; } @@ -925,7 +1003,8 @@ fn get_chain_intervals( score: max_score, num_anchors, chunk_id, - reverse_chain: anchors[smallest_id].reverse_match + reverse_chain: anchors[smallest_id].reverse_match, + overlap : 0 }; good_intervals.push(chain_interval); } @@ -938,41 +1017,70 @@ fn get_nonoverlapping_chains( let mut interval_trees = FxHashMap::default(); let mut interval_trees_ref = FxHashMap::default(); let mut good_non_overlap_intervals = vec![vec![]; num_chunks]; + let mut bases_added = 0; for (i, int) in intervals.iter().enumerate() { let q_interval = (int.interval_on_query.0)..(int.interval_on_query.1); let r_interval = (int.interval_on_ref.0)..(int.interval_on_ref.1); - let interval_tree_ref = interval_trees_ref + let interval_tree_r = interval_trees_ref .entry(int.ref_contig) .or_insert(IntervalTree::new()); let interval_tree_q = interval_trees .entry(int.query_contig) .or_insert(IntervalTree::new()); + let mut sum_overlaps_ref = 0; + let mut sum_overlaps_query = 0; let no_overlap_ref; - if interval_tree_ref.find(&r_interval).count() == 0 { + if interval_tree_r.find(&r_interval).count() == 0 { no_overlap_ref = true } else { - no_overlap_ref = false; +// let mut TODO_intervals= vec![]; + let overlaps = interval_tree_r.find(&r_interval); + let mut small_ol = false; + for ol in overlaps { + let ol_interval: &ChainInterval = &intervals[*ol.data()]; + let overlap = GnPosition::min( + int.interval_on_ref.1 - ol_interval.interval_on_ref.0, + ol_interval.interval_on_ref.1 - int.interval_on_ref.0, + ); + sum_overlaps_ref += overlap; +// TODO_intervals.push(ol_interval.clone()); + + } + if (sum_overlaps_ref as f32) < int.ref_range_len() as f32 * OVERLAP_ORTHOLOGOUS_FRACTION { + bases_added += int.query_range_len(); + small_ol = true; +// dbg!("ref", TODO_intervals, int); + } + if small_ol { + no_overlap_ref = true; + } else { + no_overlap_ref = false; + } } let no_overlap_query; if interval_tree_q.find(&q_interval).count() == 0 { no_overlap_query = true; } else { -// let overlaps = interval_tree_q.find(&q_interval); - let small_ol = false; - // for ol in overlaps { - // let ol_interval = &intervals[*ol.data()]; - // let interval_length = ol_interval.query_range_len(); - // let overlap = GnPosition::min( - // int.interval_on_query.1 - ol_interval.interval_on_query.0, - // ol_interval.interval_on_query.1 - int.interval_on_query.0, - // ); - // if (overlap as f64) < -1. { - // //interval_length as f64 * 0.00 { - // small_ol = true; - // } - // } + let overlaps = interval_tree_q.find(&q_interval); + let mut small_ol = false; +// let mut TODO_intervals= vec![]; + for ol in overlaps { + let ol_interval: &ChainInterval = &intervals[*ol.data()]; + let overlap = GnPosition::min( + int.interval_on_query.1 - ol_interval.interval_on_query.0, + ol_interval.interval_on_query.1 - int.interval_on_query.0, + ); + sum_overlaps_query += overlap; +// TODO_intervals.push(ol_interval.clone()); + } + + if (sum_overlaps_query as f32) < int.query_range_len() as f32 * OVERLAP_ORTHOLOGOUS_FRACTION { + bases_added += int.query_range_len(); + small_ol = true; +// dbg!("query", TODO_intervals, int); + } if small_ol { no_overlap_query = true; } else { @@ -980,14 +1088,16 @@ fn get_nonoverlapping_chains( } } if no_overlap_ref && no_overlap_query { - // if no_overlap_query{ // interval_tree_q.insert(q_interval, i); - interval_tree_ref.insert(r_interval, i); + interval_tree_r.insert(r_interval, i); + let mut cloned_int = int.clone(); + cloned_int.overlap = sum_overlaps_query; good_non_overlap_intervals[int.chunk_id].push(int.clone()); } } + debug!("Bases rescued by small overlapping orthologous threshold: {}", bases_added); //good_non_overlap_intervals.sort_by(|x, y| y.partial_cmp(&x).unwrap()); good_non_overlap_intervals } diff --git a/src/cmd_line.rs b/src/cmd_line.rs index 44b7bb1..551fc70 100644 --- a/src/cmd_line.rs +++ b/src/cmd_line.rs @@ -12,11 +12,11 @@ pub const H_IND_CTG_REF: &str = "Use individual sequences for the REFERENCE in a pub const FULL_INDEX: &str = "marker index"; pub const CMD_FULL_INDEX: &str = "marker-index"; -pub const H_FULL_INDEX: &str = "Loads a larger index for faster filtering. Uses more memory and takes longer to load, but faster for many all-to-all comparisons.\t[default: load index if > 50 query files, don't load otherwise]"; +pub const H_FULL_INDEX: &str = "Hash-table inverted index for faster ANI filtering. \t[default: load index if > 50 query files]"; pub const ROBUST: &str = "robust"; pub const CMD_ROBUST: &str = "robust"; -pub const H_ROBUST: &str = "Robust ani estimation; estimate mean after trim off 10%/90% quantiles."; +pub const H_ROBUST: &str = "Estimate mean after trim off 10%/90% quantiles."; pub const FULL_MAT: &str = "full-matrix"; pub const CMD_FULL_MAT: &str = "full-matrix"; @@ -28,11 +28,37 @@ pub const H_KEEP_REFS: &str = "Keep reference sketches in memory if the sketch p pub const C_FACTOR: &str = "c"; pub const CMD_C_FACTOR: &str = "c"; -pub const H_C_FACTOR: &str = "Compression factor. Memory usage and runtime is inversely proportional to c. Lower c allows for ANI comparison of more distant genomes.\t[default: 125]"; +pub const H_C_FACTOR: &str = "Compression factor (k-mer subsampling rate).\t[default: 125]"; -pub const H_SCREEN: &str = "Screen out pairs with < % identity using a hash table in constant time.\t[default: 80]"; +pub const H_SCREEN: &str = "Screen out pairs with < % identity using k-mer sketching.\t[default: 80]"; pub const CONF_INTERVAL: &str = "ci"; pub const CMD_CONF_INTERVAL: &str = "ci"; pub const H_CONF_INTERVAL: &str = "Output [5%,95%] ANI confidence intervals using percentile bootstrap on the putative ANI distribution."; pub const H_CONF_INTERVAL_TRI: &str = "Output [5%,95%] ANI confidence intervals using percentile bootstrap on the putative ANI distribution. Only works with --sparse or -E."; + +pub const LEARNED_ANI: &str = "learned-regression-model"; +pub const CMD_LEARNED_ANI : &str = "learned-ani"; +pub const H_LEARNED_ANI: &str = "Use ANI prediction with a regression model trained on MAG data. \t[default: on if c > 70]"; + +pub const NO_LEARNED_ANI: &str = "no-learned-regression-model"; +pub const CMD_NO_LEARNED_ANI : &str = "no-learned-ani"; +pub const H_NO_LEARNED_ANI: &str = "Disable regression model for ANI prediction.\t[default: disabled unless c > 70]"; + +pub const MODE_SLOW: &str = "slow"; +pub const CMD_MODE_SLOW : &str = "slow"; +pub const H_MODE_SLOW : &str = "Slower skani mode; 4x slower and more memory. Gives more accurate AF and sometimes (but not always) more accurate ANI for very messy assemblies (e.g. eukaryotes, low-quality assemblies) and low ANI genomes. Alias for -c 30."; + +pub const MODE_FAST: &str = "fast"; +pub const CMD_MODE_FAST : &str = "fast"; +pub const H_MODE_FAST : &str = "Faster skani mode; 2x faster and less memory. Less accurate AF and sometimes less accurate ANI for distant genomes. Alias for -c 200."; + +pub const MARKER_C: &str = "marker_c"; +pub const CMD_MARKER_C: char = 'm'; +pub const H_MARKER_C: &str = "Marker k-mer compression factor. Markers are used for filtering. Consider decreasing if genome is small or mapping individual small contigs. \t[default: 1000]"; + +pub const DETAIL_OUT: &str = "detailed"; +pub const CMD_DETAIL_OUT: &str = "detailed"; +pub const H_DETAIL_OUT: &str = "Output detailed ANI/AF info for debugging."; + + diff --git a/src/dist.rs b/src/dist.rs index d30587e..2672af5 100644 --- a/src/dist.rs +++ b/src/dist.rs @@ -1,4 +1,5 @@ use crate::chain; +use crate::regression; use crate::file_io; use crate::params::*; use crate::screen; @@ -9,7 +10,6 @@ use std::sync::Mutex; use std::time::Instant; pub fn dist(command_params: CommandParams, mut sketch_params: SketchParams) { - //TODO let ref_sketches; let query_params; let query_sketches; @@ -140,13 +140,22 @@ pub fn dist(command_params: CommandParams, mut sketch_params: SketchParams) { info!("{} query sequences processed.", locked); } }); - let anis = anis.into_inner().unwrap(); + let mut anis = anis.into_inner().unwrap(); + let model_opt = regression::get_model(sketch_params.c, command_params.learned_ani); + if model_opt.is_some(){ + info!("{}",LEARNED_INFO_HELP); + let model = model_opt.as_ref().unwrap(); + for ani in anis.iter_mut(){ + regression::predict_from_ani_res(ani, &model); + } + } file_io::write_query_ref_list( &anis, &command_params.out_file_name, command_params.max_results, sketch_params.use_aa, command_params.est_ci, + command_params.detailed_out, ); info!("ANI calculation time: {}", now.elapsed().as_secs_f32()); } diff --git a/src/file_io.rs b/src/file_io.rs index 5f88dce..a725b4c 100644 --- a/src/file_io.rs +++ b/src/file_io.rs @@ -12,16 +12,18 @@ use std::fs::File; use std::io::{self, BufReader, BufWriter, Write}; use std::sync::Mutex; -fn write_header(writer: &mut impl Write, id_str: &str, ci: bool) { - if !ci { +fn write_header(writer: &mut impl Write, id_str: &str, ci: bool, verbose: bool) { + if !ci && !verbose { writeln!(writer,"Ref_file\tQuery_file\t{}\tAlign_fraction_ref\tAlign_fraction_query\tRef_name\tQuery_name", id_str).unwrap(); - } else { + } else if !verbose { writeln!(writer,"Ref_file\tQuery_file\t{}\tAlign_fraction_ref\tAlign_fraction_query\tRef_name\tQuery_name\t{}_5_percentile\t{}_95_percentile", id_str, id_str, id_str).unwrap(); + } else { + writeln!(writer,"Ref_file\tQuery_file\t{}\tAlign_fraction_ref\tAlign_fraction_query\tRef_name\tQuery_name\tNum_ref_contigs\tNum_query_contigs\t{}_5_percentile\t{}_95_percentile\tStandard_deviation\tRef_90_ctg_len\tRef_50_ctg_len\tRef_10_ctg_len\tQuery_90_ctg_len\tQuery_50_ctg_len\tQuery_10_ctg_len\tAvg_chain_len\tTotal_bases_covered", id_str, id_str, id_str).unwrap(); } } -fn write_ani_res(writer: &mut impl Write, ani_res: &AniEstResult, ci: bool) { - if !ci { +fn write_ani_res(writer: &mut impl Write, ani_res: &AniEstResult, ci: bool, verbose: bool) { + if !ci && !verbose { writeln!( writer, "{}\t{}\t{:.2}\t{:.2}\t{:.2}\t{}\t{}", @@ -34,7 +36,7 @@ fn write_ani_res(writer: &mut impl Write, ani_res: &AniEstResult, ci: bool) { ani_res.query_contig, ) .unwrap(); - } else { + } else if !verbose { writeln!( writer, "{}\t{}\t{:.2}\t{:.2}\t{:.2}\t{}\t{}\t{:.2}\t{:.2}", @@ -49,6 +51,32 @@ fn write_ani_res(writer: &mut impl Write, ani_res: &AniEstResult, ci: bool) { ani_res.ci_upper * 100., ) .unwrap(); + } else { + writeln!( + writer, + "{}\t{}\t{:.2}\t{:.2}\t{:.2}\t{}\t{}\t{}\t{}\t{:.2}\t{:.2}\t{:.2}\t{:0}\t{:0}\t{:0}\t{:0}\t{:0}\t{:0}\t{:0}\t{:0}", + ani_res.ref_file, + ani_res.query_file, + ani_res.ani * 100., + ani_res.align_fraction_ref * 100., + ani_res.align_fraction_query * 100., + ani_res.ref_contig, + ani_res.query_contig, + ani_res.num_contigs_r, + ani_res.num_contigs_q, + ani_res.ci_lower * 100., + ani_res.ci_upper * 100., + ani_res.std * 100., + ani_res.quant_90_contig_len_r, + ani_res.quant_50_contig_len_r, + ani_res.quant_10_contig_len_r, + ani_res.quant_90_contig_len_q, + ani_res.quant_50_contig_len_q, + ani_res.quant_10_contig_len_q, + ani_res.avg_chain_int_len, + ani_res.total_bases_covered, + ) + .unwrap(); } } @@ -105,10 +133,21 @@ pub fn fastx_to_sketches( seed, ) } else { - #[cfg(any(target_arch = "x86", target_arch = "x86_64"))] - if is_x86_feature_detected!("avx2") && true{ - unsafe { - seeding::avx2_fmh_seeds( + #[cfg(any(target_arch = "x86_64"))] + { + if is_x86_feature_detected!("avx2"){ + use crate::avx2_seeding; + unsafe { + avx2_seeding::avx2_fmh_seeds( + &seq, + sketch_params, + j as u32, + &mut new_sketch, + seed, + ); + } + } else { + seeding::fmh_seeds( &seq, sketch_params, j as u32, @@ -116,15 +155,18 @@ pub fn fastx_to_sketches( seed, ); } - } else { - seeding::fmh_seeds( - &seq, - sketch_params, - j as u32, - &mut new_sketch, - seed, - ); } + #[cfg(not(target_arch = "x86_64"))] + { + seeding::fmh_seeds( + &seq, + sketch_params, + j as u32, + &mut new_sketch, + seed, + ); + } + } //new_sketch.contig_order = 0; j += 1; @@ -137,10 +179,11 @@ pub fn fastx_to_sketches( } } if is_valid { - if new_sketch.total_sequence_length > 20000000 { - new_sketch.repetitive_kmers = - seeding::get_repetitive_kmers(&new_sketch.kmer_seeds_k); - } +// if new_sketch.total_sequence_length > REPET_KMER_THRESHOLD{ +// new_sketch.repetitive_kmers = +// seeding::get_repetitive_kmers(&new_sketch.kmer_seeds_k, new_sketch.c); +// debug!("Repetitive cutoff multiplicity is {} for {}", new_sketch.repetitive_kmers, ref_file); +// } { let mut locked = ref_sketches.lock().unwrap(); @@ -201,10 +244,21 @@ pub fn fastx_to_multiple_sketch_rewrite( seed, ) } else { - #[cfg(any(target_arch = "x86", target_arch = "x86_64"))] - if is_x86_feature_detected!("avx2") { - unsafe { - seeding::avx2_fmh_seeds( + #[cfg(any(target_arch = "x86_64"))] + { + if is_x86_feature_detected!("avx2") { + use crate::avx2_seeding; + unsafe { + avx2_seeding::avx2_fmh_seeds( + &seq, + sketch_params, + 0_u32, + &mut new_sketch, + seed, + ); + } + } else { + seeding::fmh_seeds( &seq, sketch_params, 0_u32, @@ -212,17 +266,25 @@ pub fn fastx_to_multiple_sketch_rewrite( seed, ); } - } else { - seeding::fmh_seeds( - &seq, - sketch_params, - 0_u32, - &mut new_sketch, - seed, - ); + } + #[cfg(not(target_arch = "x86_64"))] + { + seeding::fmh_seeds( + &seq, + sketch_params, + j as u32, + &mut new_sketch, + seed, + ); } } new_sketch.contig_order = j; + +// if new_sketch.total_sequence_length > REPET_KMER_THRESHOLD { +// new_sketch.repetitive_kmers = +// seeding::get_repetitive_kmers(&new_sketch.kmer_seeds_k, new_sketch.c); +// } + let mut locked = ref_sketches.lock().unwrap(); locked.push(new_sketch); j += 1; @@ -302,7 +364,7 @@ pub fn write_phyllip_matrix( for j in 0..end { if i == j { write!(&mut af_file, "\t{:.2}", 100.).unwrap(); - continue + continue; } let x = usize::min(i, j); let y = usize::max(i, j); @@ -355,10 +417,10 @@ pub fn write_phyllip_matrix( end = i; } for j in 0..end { - if i == j{ + if i == j { write!(&mut ani_file, "\t{:.2}", 100.).unwrap(); write!(&mut af_file, "\t{:.2}", 100.).unwrap(); - continue + continue; } let x = usize::min(i, j); let y = usize::max(i, j); @@ -405,28 +467,29 @@ pub fn write_sparse_matrix( file_name: &str, aai: bool, est_ci: bool, + detailed_out: bool, ) { let id_str = if aai { "AAI" } else { "ANI" }; if file_name.is_empty() { let stdout = io::stdout(); let mut handle = stdout.lock(); - write_header(&mut handle, id_str, est_ci); + write_header(&mut handle, id_str, est_ci, detailed_out); // write!(&mut handle,"Ref_file\tQuery_file\t{}\tAlign_fraction_ref\tAlign_fraction_query\t{}_95_percentile\t{}_5_percentile\tRef_name\tQuery_name\n", id_str, id_str, id_str).unwrap(); for i in anis.keys() { for (j, ani_res) in anis[i].iter() { if !(anis[i][j].ani == -1. || anis[i][j].ani.is_nan()) { - write_ani_res(&mut handle, ani_res, est_ci); + write_ani_res(&mut handle, ani_res, est_ci, detailed_out); } } } } else { let ani_mat_file = file_name.to_string(); let mut ani_file = BufWriter::new(File::create(ani_mat_file).expect(file_name)); - write_header(&mut ani_file, id_str, est_ci); + write_header(&mut ani_file, id_str, est_ci, detailed_out); for i in anis.keys() { for (j, ani_res) in anis[i].iter() { if !(anis[i][j].ani == -1. || anis[i][j].ani.is_nan()) { - write_ani_res(&mut ani_file, ani_res, est_ci); + write_ani_res(&mut ani_file, ani_res, est_ci, detailed_out); } } } @@ -439,6 +502,7 @@ pub fn write_query_ref_list( n: usize, aai: bool, est_ci: bool, + detailed_out: bool, ) { let id_str = if aai { "AAI" } else { "ANI" }; let mut query_file_result_map = FxHashMap::default(); @@ -464,25 +528,25 @@ pub fn write_query_ref_list( if out_file.is_empty() { let stdout = io::stdout(); let mut handle = stdout.lock(); - write_header(&mut handle, id_str, est_ci); + write_header(&mut handle, id_str, est_ci, detailed_out); for key in sorted_keys { let mut anis = query_file_result_map[key].clone(); anis.sort_by(|y, x| x.ani.partial_cmp(&y.ani).unwrap()); for i in 0..usize::min(n, anis.len()) { - write_ani_res(&mut handle, anis[i], est_ci); + write_ani_res(&mut handle, anis[i], est_ci, detailed_out); } } } else { let mut handle; handle = File::create(out_file).expect(file_name); - write_header(&mut handle, id_str, est_ci); + write_header(&mut handle, id_str, est_ci, detailed_out); for key in sorted_keys { let mut anis = query_file_result_map[key].clone(); anis.sort_by(|y, x| x.ani.partial_cmp(&y.ani).unwrap()); for i in 0..usize::min(n, anis.len()) { - write_ani_res(&mut handle, anis[i], est_ci); + write_ani_res(&mut handle, anis[i], est_ci, detailed_out); } } } diff --git a/src/lib.rs b/src/lib.rs index 280992f..46a277d 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -10,3 +10,8 @@ pub mod sketch; pub mod dist; pub mod triangle; pub mod cmd_line; +pub mod model; +pub mod regression; + +#[cfg(target_arch = "x86_64")] +pub mod avx2_seeding; diff --git a/src/main.rs b/src/main.rs index 7c28333..2daff6c 100644 --- a/src/main.rs +++ b/src/main.rs @@ -8,17 +8,20 @@ use skani::search; use skani::sketch; use skani::triangle; -//Use this allocator instead of the default +//Use this allocator when statically compiling +//instead of the default //because the musl statically compiled binary //uses a bad default allocator which makes the -//binary take 60% longer!!! +//binary take 60% longer!!! Only affects +//static compilation though. +#[cfg(target_env = "x86_64")] #[global_allocator] static GLOBAL: tikv_jemallocator::Jemalloc = tikv_jemallocator::Jemalloc; fn main() { let matches = Command::new("skani") .setting(AppSettings::ArgRequiredElseHelp) - .version("0.0.1") + .version("0.1.0") .about("fast, robust ANI calculation and database searching for metagenomic contigs and assemblies. \n\nQuick ANI calculation:\nskani dist genome1.fa genome2.fa \n\nMemory-efficient database search:\nskani sketch genomes/* -o database; skani search -d database query1.fa query2.fa ...\n\nAll-to-all comparison:\nskani triangle genomes/*") .subcommand( SubCommand::with_name("help").setting(AppSettings::Hidden) @@ -32,11 +35,7 @@ fn main() { .help("Number of threads. ") .takes_value(true), ) - .arg( - Arg::new("avx2") - .long("avx2") - ) - .about("Sketch (index) genomes. Usage: skani sketch genome1.fa genome2.fa ... -o new_sketch_folder") + .about("Sketch (index) genomes.\nUsage: skani sketch genome1.fa genome2.fa ... -o new_sketch_folder") .help_heading("INPUT/OUTPUT") .arg( Arg::new("fasta_files") @@ -52,6 +51,19 @@ fn main() { .takes_value(true), ) .arg(Arg::new("output sketch folder").short('o').help("Output folder where sketch files are placed. Creates a folder if it does not exist, and overwrites the contents in folder if it does.").takes_value(true).required(true).display_order(1)) + .help_heading("PRESETS") + .arg( + Arg::new(MODE_SLOW) + .long(CMD_MODE_SLOW) + .help(H_MODE_SLOW) + .takes_value(false), + ) + .arg( + Arg::new(MODE_FAST) + .long(CMD_MODE_FAST) + .help(H_MODE_FAST) + .takes_value(false), + ) .help_heading("SKETCH PARAMETERS") .arg( Arg::new("aai") @@ -73,10 +85,11 @@ fn main() { .help(H_C_FACTOR) .takes_value(true), ) + .arg( - Arg::new("marker_c") - .short('m') - .help("Marker k-mer compression factor. Markers are used for filtering. You want at least ~100 markers, so genome_size/marker_c > 100 is highly recommended. Higher value is more time/memory efficient. \t[default: 1000] ") + Arg::new(MARKER_C) + .short(CMD_MARKER_C) + .help(H_MARKER_C) .takes_value(true), ) .group( @@ -93,7 +106,7 @@ fn main() { ) .subcommand( SubCommand::with_name(params::DIST_STRING) - .about("Compute ANI for queries against references fasta files or pre-computed sketch files. Usage: skani dist query.fa ref1.fa ref2.fa ... or use -q/--ql and -r/--rl options.") + .about("Compute ANI for queries against references fasta files or pre-computed sketch files.\nUsage: skani dist query.fa ref1.fa ref2.fa ... or use -q/--ql and -r/--rl options.") .arg( Arg::new("t") .short('t') @@ -183,12 +196,44 @@ fn main() { Arg::new(CONF_INTERVAL) .long(CMD_CONF_INTERVAL) .help(H_CONF_INTERVAL) + .takes_value(false) + ) + .arg( + Arg::new(DETAIL_OUT) + .long(CMD_DETAIL_OUT) + .help(H_DETAIL_OUT) + .takes_value(false) + ) + .help_heading("PRESETS") + .arg( + Arg::new(MODE_SLOW) + .long(CMD_MODE_SLOW) + .help(H_MODE_SLOW) + .takes_value(false), + ) + .arg( + Arg::new(MODE_FAST) + .long(CMD_MODE_FAST) + .help(H_MODE_FAST) + .takes_value(false), ) .help_heading("ALGORITHM PARAMETERS") .arg( - Arg::new("marker_c") - .short('m') - .help("Marker k-mer compression factor. Markers are used for filtering. You want at least ~100 markers, so genome_size/marker_c > 100 is highly recommended. Higher value is more time/memory efficient. \t[default: 1000] ") + Arg::new(LEARNED_ANI) + .long(CMD_LEARNED_ANI) + .help(H_LEARNED_ANI) + .takes_value(false) + ) + .arg( + Arg::new(NO_LEARNED_ANI) + .long(CMD_NO_LEARNED_ANI) + .help(H_NO_LEARNED_ANI) + .takes_value(false) + ) + .arg( + Arg::new(MARKER_C) + .short(CMD_MARKER_C) + .help(H_MARKER_C) .takes_value(true), ) .arg( @@ -241,7 +286,7 @@ fn main() { ) .subcommand( SubCommand::with_name(params::TRIANGLE_STRING) - .about("Compute a lower triangular distance ANI/AF matrix. Usage: skani triangle genome1.fa genome2.fa genome3.fa ...") + .about("Compute a lower triangular distance ANI/AF matrix.\nUsage: skani triangle genome1.fa genome2.fa genome3.fa ...") .arg( Arg::new("t") .short('t') @@ -298,6 +343,13 @@ fn main() { Arg::new(CONF_INTERVAL) .long(CMD_CONF_INTERVAL) .help(H_CONF_INTERVAL_TRI) + .takes_value(false) + ) + .arg( + Arg::new(DETAIL_OUT) + .long(CMD_DETAIL_OUT) + .help(H_DETAIL_OUT) + .takes_value(false) ) .arg( Arg::new("sparse") @@ -305,11 +357,37 @@ fn main() { .short('E') .help("Output comparisons in a row-by-row form (i.e. sparse matrix) in the same form as `skani dist`. Only pairs with aligned fraction > --min-af are output."), ) + .help_heading("PRESETS") + .arg( + Arg::new(MODE_SLOW) + .long(CMD_MODE_SLOW) + .help(H_MODE_SLOW) + .takes_value(false), + ) + .arg( + Arg::new(MODE_FAST) + .long(CMD_MODE_FAST) + .help(H_MODE_FAST) + .takes_value(false), + ) + .help_heading("ALGORITHM PARAMETERS") .arg( - Arg::new("marker_c") - .short('m') - .help("Marker k-mer compression factor. Markers are used for filtering. You want at least ~100 markers, so genome_size/marker_c > 100 is highly recommended. Higher value is more time/memory efficient. \t[default: 1000] ") + Arg::new(LEARNED_ANI) + .long(CMD_LEARNED_ANI) + .help(H_LEARNED_ANI) + .takes_value(false) + ) + .arg( + Arg::new(NO_LEARNED_ANI) + .long(CMD_NO_LEARNED_ANI) + .help(H_NO_LEARNED_ANI) + .takes_value(false) + ) + .arg( + Arg::new(MARKER_C) + .short(CMD_MARKER_C) + .help(H_MARKER_C) .takes_value(true), ) .arg(Arg::new("s").short('s').takes_value(true).help(H_SCREEN)) @@ -348,7 +426,7 @@ fn main() { ) .subcommand( SubCommand::with_name(params::SEARCH_STRING) - .about("Search queries against a large pre-sketched database of reference genomes in a memory efficient manner. Algorithm parameters are determined by skani sketch parameters. Usage: skani search -d sketch_folder query1.fa query2.fa ... ") + .about("Search queries against a large pre-sketched database of reference genomes in a memory efficient manner.\nUsage: skani search -d sketch_folder query1.fa query2.fa ... ") .arg( Arg::new("t") .short('t') @@ -401,6 +479,13 @@ fn main() { Arg::new(CONF_INTERVAL) .long(CMD_CONF_INTERVAL) .help(H_CONF_INTERVAL) + .takes_value(false) + ) + .arg( + Arg::new(DETAIL_OUT) + .long(CMD_DETAIL_OUT) + .help(H_DETAIL_OUT) + .takes_value(false) ) .arg( Arg::new(MIN_ALIGN_FRAC) @@ -422,6 +507,18 @@ fn main() { .required(true), ) .help_heading("ALGORITHM PARAMETERS") + .arg( + Arg::new(LEARNED_ANI) + .long(CMD_LEARNED_ANI) + .help(H_LEARNED_ANI) + .takes_value(false) + ) + .arg( + Arg::new(NO_LEARNED_ANI) + .long(CMD_NO_LEARNED_ANI) + .help(H_NO_LEARNED_ANI) + .takes_value(false) + ) .arg( Arg::new(KEEP_REFS) .long(CMD_KEEP_REFS) @@ -455,7 +552,6 @@ fn main() { let cmd_txt = env::args().into_iter().collect::>().join(" "); log::info!("{}", cmd_txt); - //SKETCHING if command_params.mode == params::Mode::Sketch { sketch::sketch(command_params, sketch_params); } else if command_params.mode == params::Mode::Search { diff --git a/src/model.rs b/src/model.rs new file mode 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+ diff --git a/src/params.rs b/src/params.rs index ac6b701..385b344 100644 --- a/src/params.rs +++ b/src/params.rs @@ -20,10 +20,10 @@ pub const D_LENGTH_CUTOFF: usize = D_FRAGMENT_LENGTH; pub const D_FRAC_COVER_CUTOFF: &str = "15"; pub const D_ANI_AND_COVER_CUTOFF: f64 = 0.95; pub const D_FRAC_COVER_CUTOFF_AA: &str = "5"; -pub const D_CHAIN_BAND: usize = 25; -pub const D_CHAIN_BAND_AAI: usize = 125; +//pub const D_CHAIN_BAND: usize = 50; +//pub const D_CHAIN_BAND_AAI: usize = 125; pub const ORF_SIZE: usize = 30; -pub const MARKER_C: &str = "1000"; +pub const MARKER_C_DEFAULT: &str = "1000"; pub const K_MARKER_AA: usize = 10; pub const K_MARKER_DNA: usize = 21; pub const SEARCH_STRING: &str = "search"; @@ -40,6 +40,13 @@ pub const BP_CHAIN_BAND_AAI: usize = 500; pub const SEARCH_AAI_CUTOFF_DEFAULT: f64 = 0.60; pub const SEARCH_ANI_CUTOFF_DEFAULT: f64 = 0.80; pub const FULL_INDEX_THRESH: usize = 50; +pub const REPET_KMER_THRESHOLD: usize = 8_000_000; +pub const OVERLAP_ORTHOLOGOUS_FRACTION: f32 = 0.50; +pub const TOTAL_BASES_REGRESS_CUTOFF: usize = 150000; +pub const LEARNED_INFO_HELP: &str = "Learned ANI mode detected. ANI may be adjusted according to a regression model trained on MAGs."; + +pub const FAST_C: usize = 200; +pub const SLOW_C: usize = 30; #[derive(PartialEq)] @@ -59,7 +66,7 @@ pub struct MapParams { pub length_cutoff: usize, pub frac_cover_cutoff: f64, pub length_cover_cutoff: usize, - pub chain_band: usize, + pub index_chain_band: usize, pub k: usize, pub amino_acid: bool, pub min_score: f64, @@ -88,7 +95,10 @@ pub struct CommandParams{ pub individual_contig_r: bool, pub min_aligned_frac: f64, pub keep_refs: bool, - pub est_ci: bool + pub est_ci: bool, + pub learned_ani: bool, + pub learned_ani_cmd: bool, + pub detailed_out: bool } pub fn fragment_length_formula(_n: usize, aa: bool) -> usize { diff --git a/src/parse.rs b/src/parse.rs index cd9b95f..28284eb 100644 --- a/src/parse.rs +++ b/src/parse.rs @@ -1,12 +1,20 @@ -use crate::params::*; use crate::cmd_line::*; +use crate::params::*; use clap::parser::ArgMatches; use log::LevelFilter; use log::*; use std::fs; use std::fs::File; use std::io::{prelude::*, BufReader}; - +pub fn use_learned_ani(c: usize, individual_contig_q: bool, individual_contig_r: bool, median: bool, robust: bool) -> bool{ + let learned_ani; + if c >= 70 && !individual_contig_q && !individual_contig_r && !median && !robust{ + learned_ani = true; + } else { + learned_ani = false; + } + learned_ani +} pub fn parse_params(matches: &ArgMatches) -> (SketchParams, CommandParams) { let mode; let matches_subc; @@ -140,36 +148,69 @@ pub fn parse_params(matches: &ArgMatches) -> (SketchParams, CommandParams) { .unwrap_or(def_k) .parse::() .unwrap(); - + let use_syncs = false; - let c = matches_subc + let mut c = matches_subc .value_of("c") .unwrap_or(def_c) .parse::() .unwrap(); + if matches_subc.is_present(MODE_FAST) && + matches_subc.is_present(MODE_SLOW){ + panic!("Both --slow and --fast were set. This is not allowed."); + } + if matches_subc.is_present(MODE_FAST){ + if matches_subc.is_present("c"){ + warn!("-c value is set but --fast is also set. Using --fast mode instead (-c 200)"); + } + c = FAST_C + } + if matches_subc.is_present(MODE_SLOW){ + if matches_subc.is_present("c"){ + warn!("-c value is set but --slow is also set. Using --slow mode instead (-c 30)"); + } + c = SLOW_C + } let min_aligned_frac; let est_ci; - if mode != Mode::Sketch{ - let def_maf = if amino_acid{ D_FRAC_COVER_CUTOFF_AA} else {D_FRAC_COVER_CUTOFF}; - min_aligned_frac = matches_subc.value_of(MIN_ALIGN_FRAC).unwrap_or(def_maf).parse::().unwrap()/100.; + let detailed_out; + if mode != Mode::Sketch { + let def_maf = if amino_acid { + D_FRAC_COVER_CUTOFF_AA + } else { + D_FRAC_COVER_CUTOFF + }; + min_aligned_frac = matches_subc + .value_of(MIN_ALIGN_FRAC) + .unwrap_or(def_maf) + .parse::() + .unwrap() + / 100.; est_ci = matches_subc.is_present(CONF_INTERVAL); - } - else{ + detailed_out = matches_subc.is_present(DETAIL_OUT); + } else { min_aligned_frac = 0.; est_ci = false; + detailed_out = false; } - let marker_c = matches_subc.value_of("marker_c").unwrap_or(MARKER_C).parse::().unwrap(); + let marker_c = matches_subc + .value_of("marker_c") + .unwrap_or(MARKER_C_DEFAULT) + .parse::() + .unwrap(); let out_file_name; if mode == Mode::Triangle { out_file_name = matches_subc.value_of("output").unwrap_or("").to_string(); } else if mode == Mode::Sketch { - out_file_name = matches_subc.value_of("output sketch folder").unwrap_or("").to_string(); + out_file_name = matches_subc + .value_of("output sketch folder") + .unwrap_or("") + .to_string(); } else if mode == Mode::Dist { out_file_name = matches_subc.value_of("output").unwrap_or("").to_string(); - } - else{ + } else { panic!("Mode doesn't exist"); } @@ -177,7 +218,12 @@ pub fn parse_params(matches: &ArgMatches) -> (SketchParams, CommandParams) { let mut robust = false; let mut median = false; if mode == Mode::Triangle || mode == Mode::Dist { - screen_val = matches_subc.value_of("s").unwrap_or("0.00").parse::().unwrap() / 100.; + screen_val = matches_subc + .value_of("s") + .unwrap_or("0.00") + .parse::() + .unwrap() + / 100.; } if mode == Mode::Triangle || mode == Mode::Search || mode == Mode::Dist { robust = matches_subc.is_present("robust"); @@ -188,7 +234,10 @@ pub fn parse_params(matches: &ArgMatches) -> (SketchParams, CommandParams) { let mut refs_are_sketch = !ref_files.is_empty(); for ref_file in ref_files.iter() { - if !ref_file.contains(".sketch") && !ref_file.contains(".marker") && !ref_file.contains("markers.bin"){ + if !ref_file.contains(".sketch") + && !ref_file.contains(".marker") + && !ref_file.contains("markers.bin") + { refs_are_sketch = false; break; } @@ -202,53 +251,65 @@ pub fn parse_params(matches: &ArgMatches) -> (SketchParams, CommandParams) { } } - let individual_contig_q; let individual_contig_r; - if mode == Mode::Triangle{ - if matches_subc.is_present("individual contig"){ + if mode == Mode::Triangle { + if matches_subc.is_present("individual contig") { individual_contig_q = true; individual_contig_r = true; - } - else{ + } else { individual_contig_q = false; individual_contig_r = false; } - } - else if mode == Mode::Dist{ + } else if mode == Mode::Dist { individual_contig_q = matches_subc.is_present("individual contig query"); individual_contig_r = matches_subc.is_present("individual contig ref"); - } - else{ + } else { individual_contig_q = false; individual_contig_r = false; } - + let full_matrix; - if mode == Mode::Triangle{ + if mode == Mode::Triangle { full_matrix = matches_subc.is_present(FULL_MAT); - } - else{ + } else { full_matrix = false; } let screen; - if mode == Mode::Dist{ - if query_files.len() > FULL_INDEX_THRESH || individual_contig_q{ + if mode == Mode::Dist { + if query_files.len() > FULL_INDEX_THRESH || individual_contig_q { screen = true; - } - else{ + } else { screen = matches_subc.is_present(FULL_INDEX); } - } - else if mode == Mode::Triangle{ + } else if mode == Mode::Triangle { screen = true; - } - else{ + } else { screen = false; } + let learned_ani; + let learned_ani_cmd; + if mode == Mode::Triangle || mode == Mode::Dist { + if matches_subc.is_present(LEARNED_ANI) && matches_subc.is_present(NO_LEARNED_ANI) { + panic!("Only one of --learned-ani and --no-learned-ani is allowed"); + } else if matches_subc.is_present(LEARNED_ANI) { + learned_ani_cmd = true; + learned_ani = true; + } else if matches_subc.is_present(NO_LEARNED_ANI) { + learned_ani_cmd = true; + learned_ani = false; + } else { + learned_ani_cmd = false; + learned_ani = use_learned_ani(c, individual_contig_q, individual_contig_r, robust, median); + } + } else { + learned_ani_cmd = false; + learned_ani = false; + } + let command_params = CommandParams { screen, screen_val, @@ -267,7 +328,10 @@ pub fn parse_params(matches: &ArgMatches) -> (SketchParams, CommandParams) { individual_contig_r, min_aligned_frac, keep_refs: false, - est_ci + est_ci, + learned_ani, + learned_ani_cmd, + detailed_out, }; (sketch_params, command_params) @@ -327,19 +391,41 @@ pub fn parse_params_search(matches_subc: &ArgMatches) -> (SketchParams, CommandP .value_of("s") .unwrap_or("0.00") .parse::() - .unwrap()/100.; + .unwrap() + / 100.; let screen; let individual_contig_q = matches_subc.is_present("individual contig query"); - if query_files.len() > FULL_INDEX_THRESH || individual_contig_q{ + if query_files.len() > FULL_INDEX_THRESH || individual_contig_q { screen = true; - } - else{ + } else { screen = matches_subc.is_present(FULL_INDEX); } - let min_aligned_frac = matches_subc.value_of(MIN_ALIGN_FRAC).unwrap_or("-100.0").parse::().unwrap()/100.; + let min_aligned_frac = matches_subc + .value_of(MIN_ALIGN_FRAC) + .unwrap_or("-100.0") + .parse::() + .unwrap() + / 100.; let keep_refs = matches_subc.is_present(KEEP_REFS); let est_ci = matches_subc.is_present(CONF_INTERVAL); + let detailed_out = matches_subc.is_present(DETAIL_OUT); + let learned_ani; + let learned_ani_cmd; + if matches_subc.is_present(LEARNED_ANI) && matches_subc.is_present(NO_LEARNED_ANI) + { + panic!("Only one of --learned-ani and --no-learned-ani is allowed"); + } else if matches_subc.is_present(LEARNED_ANI) { + learned_ani = true; + learned_ani_cmd = true; + } else if matches_subc.is_present(NO_LEARNED_ANI) { + learned_ani = false; + learned_ani_cmd = true; + } + else{ + learned_ani = false; + learned_ani_cmd = false; + } let command_params = CommandParams { screen, @@ -360,6 +446,9 @@ pub fn parse_params_search(matches_subc: &ArgMatches) -> (SketchParams, CommandP min_aligned_frac, keep_refs, est_ci, + learned_ani, + learned_ani_cmd, + detailed_out, }; if command_params.ref_files.is_empty() { @@ -367,5 +456,7 @@ pub fn parse_params_search(matches_subc: &ArgMatches) -> (SketchParams, CommandP std::process::exit(1) } + + (SketchParams::default(), command_params) } diff --git a/src/regression.rs b/src/regression.rs new file mode 100644 index 0000000..5d5ac01 --- /dev/null +++ b/src/regression.rs @@ -0,0 +1,60 @@ +use crate::types::*; +use crate::model; +use crate::params::*; +use gbdt::decision_tree::Data; +use gbdt::gradient_boost::GBDT; +use log::*; + +pub fn get_model(c: usize, learned_ani: bool) -> Option{ + let model: Option; + if learned_ani { + if (c as i32 - 125 as i32).abs() < (c as i32 - 200 as i32).abs(){ + debug!("Using C125 regression model."); + model = Some(serde_json::from_str(model::MODEL).unwrap()); + } + else{ + debug!("Using C200 regression model."); + model = Some(serde_json::from_str(model::MODEL_C200).unwrap()); + } + } + else{ + model = None; + } + model +} + +pub fn predict_from_ani_res(ani_res: &mut AniEstResult, model: &GBDT) { + if ani_res.ani > 0.9 && ani_res.total_bases_covered > TOTAL_BASES_REGRESS_CUTOFF as GnPosition{ + let data; + if ani_res.quant_50_contig_len_r > ani_res.quant_50_contig_len_q { + data = Data::new_test_data( + vec![ + ani_res.ani * 100., + ani_res.std, + ani_res.quant_90_contig_len_r, + ani_res.quant_90_contig_len_q, + ani_res.avg_chain_int_len as f32, + ], + None, + ); + } else { + data = Data::new_test_data( + vec![ + ani_res.ani * 100., + ani_res.std, + ani_res.quant_90_contig_len_q, + ani_res.quant_90_contig_len_r, + ani_res.avg_chain_int_len as f32, + ], + None, + ); + } + let pred_ani_res = model.predict(&vec![data])[0]; + //dbg!(ani_res.ani_res*100., pred_ani_res); + if pred_ani_res < 100. { + ani_res.ci_upper = (ani_res.ci_upper - ani_res.ani) + pred_ani_res / 100.; + ani_res.ci_lower = (ani_res.ci_lower - ani_res.ani) + pred_ani_res / 100.; + ani_res.ani = pred_ani_res / 100.; + } + } +} diff --git a/src/screen.rs b/src/screen.rs index 53f7347..dc6ca4d 100644 --- a/src/screen.rs +++ b/src/screen.rs @@ -55,6 +55,10 @@ pub fn screen_refs( ref_sketches: &Vec, ) -> FxHashSet { let mut count_hash_map = FxHashMap::default(); + //Don't screen when the input sketch is too small. + if query_sketch.marker_seeds.len() < 20{ + return (0..ref_sketches.len()).collect(); + } for marker in query_sketch.marker_seeds.iter() { if kmer_to_sketch.contains_key(marker) { for sketch_id in kmer_to_sketch[marker].iter() { diff --git a/src/search.rs b/src/search.rs index c6f468a..914da9d 100644 --- a/src/search.rs +++ b/src/search.rs @@ -1,7 +1,9 @@ use crate::chain; +use crate::regression; use crate::file_io; use crate::params::*; use crate::screen; +use crate::parse; use crate::types::*; use fxhash::FxHashMap; use log::*; @@ -218,13 +220,29 @@ pub fn search(command_params: CommandParams) { if command_params.keep_refs{ info!("{} references kept in memory for --keep-refs", ref_sketches_used.read().unwrap().len()); } - let anis = anis.into_inner().unwrap(); + let mut anis = anis.into_inner().unwrap(); + let learned_ani; + if !command_params.learned_ani_cmd{ + learned_ani = parse::use_learned_ani(sketch_params.c, command_params.individual_contig_q, command_params.individual_contig_r, command_params.robust, command_params.median); + } + else{ + learned_ani = command_params.learned_ani; + } + let model_opt = regression::get_model(sketch_params.c, learned_ani); + if model_opt.is_some(){ + info!("{}",LEARNED_INFO_HELP); + let model = model_opt.as_ref().unwrap(); + for ani in anis.iter_mut(){ + regression::predict_from_ani_res(ani, &model); + } + } file_io::write_query_ref_list( &anis, &command_params.out_file_name, command_params.max_results, sketch_params.use_aa, - command_params.est_ci + command_params.est_ci, + command_params.detailed_out, ); info!("Searching time: {}", now.elapsed().as_secs_f32()); } diff --git a/src/seeding.rs b/src/seeding.rs index 16555d2..880a037 100644 --- a/src/seeding.rs +++ b/src/seeding.rs @@ -1,8 +1,5 @@ use crate::params::*; use crate::types::*; -use std::arch::x86_64::*; -//use bio::data_structures::interval_tree::IntervalTree; -//use fxhash::{hash, FxHashMap, FxHashSet}; use rust_lapper::{Interval, Lapper}; use smallvec::SmallVec; @@ -331,7 +328,10 @@ pub fn fmh_seeds( } } -pub fn get_repetitive_kmers(kmer_seeds: &Option) -> usize { +//This function is unused right now. Originally used for +//getting a repetitive k-mer masking threshold. We may +//modify the masking procedure in the future, so leaving for now. +pub fn get_repetitive_kmers(kmer_seeds: &Option, c: usize) -> usize { if kmer_seeds.is_none() { usize::MAX } else { @@ -342,268 +342,14 @@ pub fn get_repetitive_kmers(kmer_seeds: &Option) -> usize { count_vec.push(ref_pos.len()); } count_vec.sort(); - let mut max_repet_cutoff = count_vec[count_vec.len() - count_vec.len() / 10000 - 1]; - if max_repet_cutoff < 30 { - max_repet_cutoff = usize::MAX; + let mut max_repet_cutoff = count_vec[count_vec.len() - count_vec.len() / 5000 - 1]; + let default_repet_cutoff = BP_CHAIN_BAND / c; + if max_repet_cutoff < 20 || max_repet_cutoff > default_repet_cutoff{ + max_repet_cutoff = default_repet_cutoff; } max_repet_cutoff } } -#[inline] -#[target_feature(enable = "avx2")] -pub unsafe fn mm_hash256(kmer: __m256i) -> __m256i { - let mut key = kmer; - let s1 = _mm256_slli_epi64(key, 21); - key = _mm256_add_epi64(key, s1); - key = _mm256_xor_si256(key, _mm256_cmpeq_epi64(key, key)); - - key = _mm256_xor_si256(key, _mm256_srli_epi64(key, 24)); - let s2 = _mm256_slli_epi64(key, 3); - let s3 = _mm256_slli_epi64(key, 8); - - key = _mm256_add_epi64(key, s2); - key = _mm256_add_epi64(key, s3); - key = _mm256_xor_si256(key, _mm256_srli_epi64(key, 14)); - let s4 = _mm256_slli_epi64(key, 2); - let s5 = _mm256_slli_epi64(key, 4); - key = _mm256_add_epi64(key, s4); - key = _mm256_add_epi64(key, s5); - key = _mm256_xor_si256(key, _mm256_srli_epi64(key, 28)); - - let s6 = _mm256_slli_epi64(key, 31); - key = _mm256_add_epi64(key, s6); - - key -} -//use bio::data_structures::interval_tree::IntervalTree; -//use fxhash::{hash, FxHashMap, FxHashSet}; -// -#[target_feature(enable = "avx2")] -pub unsafe fn avx2_fmh_seeds( - string: &[u8], - sketch_params: &SketchParams, - contig_index: ContigIndex, - new_sketch: &mut Sketch, - seed: bool, -) { - if seed && new_sketch.kmer_seeds_k.is_none() { - new_sketch.kmer_seeds_k = Some(KmerSeeds::default()); - } - let marker_k = K_MARKER_DNA; - let kmer_seeds_k = &mut new_sketch.kmer_seeds_k; - let marker_seeds = &mut new_sketch.marker_seeds; - let k = sketch_params.k; - let c = sketch_params.c; - let marker_c = sketch_params.marker_c; - let len = (string.len() - marker_k + 1) / 4; - let string1 = &string[0..len + marker_k - 1]; - let string2 = &string[len..2 * len + marker_k - 1]; - let string3 = &string[2 * len..3 * len + marker_k - 1]; - let string4 = &string[3 * len..4 * len + marker_k - 1]; - if k > marker_k { - panic!("Value of k > {} for DNA; not allowed.", marker_k); - } - if string.len() < 2 * marker_k { - return; - } - - let mut rolling_kmer_f_marker = _mm256_set_epi64x(0, 0, 0, 0); - let mut rolling_kmer_r_marker = _mm256_set_epi64x(0, 0, 0, 0); - let rev_sub = _mm256_set_epi64x(3, 3, 3, 3); - for i in 0..marker_k - 1 { - let nuc_f1 = BYTE_TO_SEQ[string1[i] as usize] as i64; - let nuc_f2 = BYTE_TO_SEQ[string2[i] as usize] as i64; - let nuc_f3 = BYTE_TO_SEQ[string3[i] as usize] as i64; - let nuc_f4 = BYTE_TO_SEQ[string4[i] as usize] as i64; - let f_nucs = _mm256_set_epi64x(nuc_f4, nuc_f3, nuc_f2, nuc_f1); - let r_nucs = _mm256_sub_epi64(rev_sub, f_nucs); - - rolling_kmer_f_marker = _mm256_slli_epi64(rolling_kmer_f_marker, 2); - rolling_kmer_f_marker = _mm256_or_si256(rolling_kmer_f_marker, f_nucs); - - rolling_kmer_r_marker = _mm256_srli_epi64(rolling_kmer_r_marker, 2); - let shift_nuc_r = _mm256_slli_epi64(r_nucs, 40); - rolling_kmer_r_marker = _mm256_or_si256(rolling_kmer_r_marker, shift_nuc_r); - } - - let seed_mask = (MarkerBits::MAX >> (std::mem::size_of::() * 8 - 2 * k)) as i64; - let mm256_seed_mask = _mm256_set_epi64x(seed_mask, seed_mask, seed_mask, seed_mask); - let marker_mask = - (MarkerBits::MAX >> (std::mem::size_of::() * 8 - 2 * marker_k)) as i64; - let rev_marker_mask: u64 = !(3 << (2 * marker_k - 2)); - let rev_marker_mask = i64::from_le_bytes(rev_marker_mask.to_le_bytes()); - // dbg!(u64::MAX / (c as u64)); - // dbg!((u64::MAX / (c as u64)) as i64); - let threshold = i64::MIN + (u64::MAX / (c as u64)) as i64; - let _threshold_marker = i64::MIN + (u64::MAX / marker_c as u64) as i64; - let threshold_unsigned = u64::MAX / c as u64; - let threshold_marker_unsigned = u64::MAX / marker_c as u64; - let _cmp_thresh = _mm256_set_epi64x(threshold, threshold, threshold, threshold); - - let mm256_marker_mask = _mm256_set_epi64x(marker_mask, marker_mask, marker_mask, marker_mask); - let mm256_rev_marker_mask = _mm256_set_epi64x( - rev_marker_mask, - rev_marker_mask, - rev_marker_mask, - rev_marker_mask, - ); - - //dbg!(KmerEnc::print_string(u64::from_le_bytes(_mm256_extract_epi64(rolling_kmer_f_marker,0).to_le_bytes()), 21)); - - for i in marker_k-1..(len + marker_k - 1) { - let nuc_f1 = BYTE_TO_SEQ[string1[i] as usize] as i64; - let nuc_f2 = BYTE_TO_SEQ[string2[i] as usize] as i64; - let nuc_f3 = BYTE_TO_SEQ[string3[i] as usize] as i64; - let nuc_f4 = BYTE_TO_SEQ[string4[i] as usize] as i64; - let f_nucs = _mm256_set_epi64x(nuc_f4, nuc_f3, nuc_f2, nuc_f1); - let r_nucs = _mm256_sub_epi64(rev_sub, f_nucs); - rolling_kmer_f_marker = _mm256_slli_epi64(rolling_kmer_f_marker, 2); - rolling_kmer_f_marker = _mm256_or_si256(rolling_kmer_f_marker, f_nucs); - rolling_kmer_f_marker = _mm256_and_si256(rolling_kmer_f_marker, mm256_marker_mask); - rolling_kmer_r_marker = _mm256_srli_epi64(rolling_kmer_r_marker, 2); - let shift_nuc_r = _mm256_slli_epi64(r_nucs, 40); - rolling_kmer_r_marker = _mm256_and_si256(rolling_kmer_r_marker, mm256_rev_marker_mask); - rolling_kmer_r_marker = _mm256_or_si256(rolling_kmer_r_marker, shift_nuc_r); - let rolling_kmer_f_seed = _mm256_and_si256(rolling_kmer_f_marker, mm256_seed_mask); - let rolling_kmer_r_seed = _mm256_and_si256(rolling_kmer_r_marker, mm256_seed_mask); - let compare = _mm256_cmpgt_epi64(rolling_kmer_r_seed, rolling_kmer_f_seed); - let compare_marker = _mm256_cmpgt_epi64(rolling_kmer_r_marker, rolling_kmer_f_marker); - let canonical_seeds_256 = - _mm256_blendv_epi8(rolling_kmer_r_seed, rolling_kmer_f_seed, compare); - - let canonical = [ - _mm256_extract_epi64(compare, 0) != 0, - _mm256_extract_epi64(compare, 1) != 0, - _mm256_extract_epi64(compare, 2) != 0, - _mm256_extract_epi64(compare, 3) != 0, - ]; - - let canonical_seeds = [ - _mm256_extract_epi64(canonical_seeds_256, 0), - _mm256_extract_epi64(canonical_seeds_256, 1), - _mm256_extract_epi64(canonical_seeds_256, 2), - _mm256_extract_epi64(canonical_seeds_256, 3), - ]; - - let hash_256 = mm_hash256(canonical_seeds_256); - let v1 = _mm256_extract_epi64(hash_256, 0) as u64; - let v2 = _mm256_extract_epi64(hash_256, 1) as u64; - let v3 = _mm256_extract_epi64(hash_256, 2) as u64; - let v4 = _mm256_extract_epi64(hash_256, 3) as u64; - // let threshold_256 = _mm256_cmpgt_epi64(cmp_thresh, hash_256); - // let m1 = _mm256_extract_epi64(threshold_256, 0); - // let m2 = _mm256_extract_epi64(threshold_256, 1); - // let m3 = _mm256_extract_epi64(threshold_256, 2); - // let m4 = _mm256_extract_epi64(threshold_256, 3); - - if true { - // if m1 !={ - if v1 < threshold_unsigned { - const IND: i32 = 0; - let kmer_seeds = &mut kmer_seeds_k.as_mut().unwrap(); - let kmer_positions = kmer_seeds - .entry(canonical_seeds[IND as usize] as SeedBits) - .or_insert(SmallVec::<[SeedPosition; SMALL_VEC_SIZE]>::new()); - // .or_insert(vec![]); - kmer_positions.push(SeedPosition { - pos: i as GnPosition, - canonical: canonical[IND as usize], - contig_index, - phase: 0, - }); - let canonical_marker = _mm256_extract_epi64(compare_marker, IND) != 0; - let canonical_kmer_marker; - if canonical_marker { - canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_f_marker, IND); - } else { - canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_r_marker, IND); - }; - // if _mm256_extract_epi64(hash_256, IND) < threshold_marker { - if v1 < threshold_marker_unsigned { - marker_seeds.insert(canonical_kmer_marker as u64); - } - } - // if m2 != 0 { - if v2 < threshold_unsigned { - const IND: i32 = 1; - let kmer_seeds = &mut kmer_seeds_k.as_mut().unwrap(); - let kmer_positions = kmer_seeds - .entry(canonical_seeds[IND as usize] as SeedBits) - .or_insert(SmallVec::<[SeedPosition; SMALL_VEC_SIZE]>::new()); - // .or_insert(vec![]); - kmer_positions.push(SeedPosition { - pos: i as GnPosition + (len as i32 * IND) as GnPosition, - canonical: canonical[IND as usize], - contig_index, - phase: 0, - }); - let canonical_marker = _mm256_extract_epi64(compare_marker, IND) != 0; - let canonical_kmer_marker; - if canonical_marker { - canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_f_marker, IND); - } else { - canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_r_marker, IND); - }; - // if _mm256_extract_epi64(hash_256, IND) < threshold_marker { - if v2 < threshold_marker_unsigned { - marker_seeds.insert(canonical_kmer_marker as u64); - } - } - // if m3 != 0 { - if v3 < threshold_unsigned { - const IND: i32 = 2; - let kmer_seeds = &mut kmer_seeds_k.as_mut().unwrap(); - let kmer_positions = kmer_seeds - .entry(canonical_seeds[IND as usize] as SeedBits) - .or_insert(SmallVec::<[SeedPosition; SMALL_VEC_SIZE]>::new()); - // .or_insert(vec![]); - kmer_positions.push(SeedPosition { - canonical: canonical[IND as usize], - pos: i as GnPosition + (len as i32 * IND) as GnPosition, - contig_index, - phase: 0, - }); - let canonical_marker = _mm256_extract_epi64(compare_marker, IND) != 0; - let canonical_kmer_marker; - if canonical_marker { - canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_f_marker, IND); - } else { - canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_r_marker, IND); - }; - // if _mm256_extract_epi64(hash_256, IND) < threshold_marker { - if v3 < threshold_marker_unsigned { - marker_seeds.insert(canonical_kmer_marker as u64); - } - } - // if m4 != 0 { - if v4 < threshold_unsigned { - const IND: i32 = 3; - let kmer_seeds = &mut kmer_seeds_k.as_mut().unwrap(); - let kmer_positions = kmer_seeds - .entry(canonical_seeds[IND as usize] as SeedBits) - .or_insert(SmallVec::<[SeedPosition; SMALL_VEC_SIZE]>::new()); - // .or_insert(vec![]); - kmer_positions.push(SeedPosition { - pos: i as GnPosition + (len as i32 * IND) as GnPosition, - canonical: canonical[IND as usize], - contig_index, - phase: 0, - }); - let canonical_marker = _mm256_extract_epi64(compare_marker, IND) != 0; - let canonical_kmer_marker; - if canonical_marker { - canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_f_marker, IND); - } else { - canonical_kmer_marker = _mm256_extract_epi64(rolling_kmer_r_marker, IND); - }; - // if _mm256_extract_epi64(hash_256, IND) < threshold_marker { - if v4 < threshold_marker_unsigned { - marker_seeds.insert(canonical_kmer_marker as u64); - } - } - } - } -} diff --git a/src/triangle.rs b/src/triangle.rs index 16cacb7..58bef11 100644 --- a/src/triangle.rs +++ b/src/triangle.rs @@ -2,21 +2,26 @@ use crate::chain; use crate::file_io; use crate::params::*; use crate::screen; +use crate::regression; use crate::types::*; -use fxhash::{FxHashMap}; +use fxhash::FxHashMap; use log::*; use rayon::prelude::*; use std::sync::Mutex; use std::time::Instant; pub fn triangle(command_params: CommandParams, mut sketch_params: SketchParams) { + //TODO let ref_sketches; let now = Instant::now(); if command_params.refs_are_sketch { info!("Sketches detected."); - (sketch_params, ref_sketches) = file_io::sketches_from_sketch( - &command_params.ref_files, - ); + let param_and_sketches = file_io::sketches_from_sketch(&command_params.ref_files); + if param_and_sketches.0.c != sketch_params.c{ + warn!("Input parameter c = {} is not equal to the sketch parameter c = {}. Using sketch parameters.", sketch_params.c, param_and_sketches.0.c); + } + ref_sketches = param_and_sketches.1; + sketch_params = param_and_sketches.0; } else if command_params.individual_contig_r { ref_sketches = file_io::fastx_to_multiple_sketch_rewrite( &command_params.ref_files, @@ -24,8 +29,7 @@ pub fn triangle(command_params: CommandParams, mut sketch_params: SketchParams) true, ); } else { - ref_sketches = - file_io::fastx_to_sketches(&command_params.ref_files, &sketch_params, true); + ref_sketches = file_io::fastx_to_sketches(&command_params.ref_files, &sketch_params, true); } let screen_val; if command_params.screen_val == 0. { @@ -45,13 +49,16 @@ pub fn triangle(command_params: CommandParams, mut sketch_params: SketchParams) std::process::exit(1) } let kmer_to_sketch = screen::kmer_to_sketch_from_refs(&ref_sketches); - let counter : Mutex = Mutex::new(0); + let counter: Mutex = Mutex::new(0); + let model = regression::get_model(sketch_params.c, command_params.learned_ani); + if model.is_some(){ + info!("{}", LEARNED_INFO_HELP); + } (0..ref_sketches.len() - 1) .collect::>() .into_par_iter() .for_each(|i| { - let ref_sketch_i = &ref_sketches[i]; //if command_params.screen { let screened_refs = screen::screen_refs( @@ -75,7 +82,11 @@ pub fn triangle(command_params: CommandParams, mut sketch_params: SketchParams) &command_params, ); let ref_sketch_j = &ref_sketches[j]; - let ani_res = chain::chain_seeds(ref_sketch_i, ref_sketch_j, map_params); + let mut ani_res = chain::chain_seeds(ref_sketch_i, ref_sketch_j, map_params); + if command_params.learned_ani{ + let gbdt = model.as_ref().unwrap(); + regression::predict_from_ani_res(&mut ani_res, gbdt); + } let mut locked = anis.lock().unwrap(); let mapi = locked.entry(i).or_insert(FxHashMap::default()); mapi.insert(j, ani_res); @@ -83,13 +94,24 @@ pub fn triangle(command_params: CommandParams, mut sketch_params: SketchParams) }); let mut locked = counter.lock().unwrap(); *locked += 1; - if *locked % 100 == 0 && *locked != 0{ + if *locked % 100 == 0 && *locked != 0 { info!("{} query sequences processed.", locked); } }); let anis = anis.into_inner().unwrap(); + let now_pred = Instant::now(); + + debug!("Prediction time: {}", now_pred.elapsed().as_secs_f32()); + if command_params.sparse { - file_io::write_sparse_matrix(&anis, &ref_sketches, &command_params.out_file_name, sketch_params.use_aa, command_params.est_ci); + file_io::write_sparse_matrix( + &anis, + &ref_sketches, + &command_params.out_file_name, + sketch_params.use_aa, + command_params.est_ci, + command_params.detailed_out, + ); } else { file_io::write_phyllip_matrix( &anis, @@ -97,7 +119,7 @@ pub fn triangle(command_params: CommandParams, mut sketch_params: SketchParams) &command_params.out_file_name, command_params.individual_contig_r, command_params.full_matrix, - sketch_params.use_aa + sketch_params.use_aa, ); } info!("ANI triangle time: {}", now.elapsed().as_secs_f32()); diff --git a/src/types.rs b/src/types.rs index 9416b61..cd31184 100644 --- a/src/types.rs +++ b/src/types.rs @@ -119,7 +119,7 @@ pub fn mm_hash(bytes: &[u8]) -> usize { key } -#[derive(Eq, PartialEq, Ord, PartialOrd, Default, Clone, Serialize, Deserialize)] +#[derive(Eq, PartialEq, Ord, PartialOrd, Default, Clone, Serialize, Deserialize, Debug)] pub struct SeedPosition{ pub pos: GnPosition, pub canonical: bool, @@ -140,6 +140,15 @@ pub struct Sketch { pub contigs: Vec, pub total_sequence_length: usize, pub contig_lengths: Vec, + + //repetitive_kmers isn't being used right now, but we may + //make the repeat masking procedure smarter in the future. + //A repetitive k-mer threshold is set in chaining as + //2500/c. + // + //Also leaving this here so that we users can have + //valid .sketch files across versions, although we may + //break that in the future. pub repetitive_kmers: usize, pub marker_seeds: MMHashSet, pub marker_c: usize, @@ -206,7 +215,7 @@ impl Default for Sketch { contigs: vec![], total_sequence_length: 0, contig_lengths: vec![], - repetitive_kmers: usize::MAX, + repetitive_kmers: 0, marker_seeds: MMHashSet::default(), marker_c: 0, c: 0, @@ -343,7 +352,8 @@ pub struct ChainInterval { pub ref_contig: usize, pub query_contig: usize, pub chunk_id: usize, - pub reverse_chain: bool + pub reverse_chain: bool, + pub overlap: u32 } impl ChainInterval { pub fn query_range_len(&self) -> GnPosition { @@ -400,4 +410,15 @@ pub struct AniEstResult{ pub ci_upper: f32, pub ci_lower: f32, pub aai: bool, + pub quant_90_contig_len_q: f32, + pub quant_90_contig_len_r: f32, + pub quant_50_contig_len_q: f32, + pub quant_50_contig_len_r: f32, + pub quant_10_contig_len_q: f32, + pub quant_10_contig_len_r: f32, + pub std: f32, + pub num_contigs_q: u32, + pub num_contigs_r: u32, + pub avg_chain_int_len: u32, + pub total_bases_covered: u32, } diff --git a/test_files/TOPAZ_IOD1_E001.fna.gz b/test_files/TOPAZ_IOD1_E001.fna.gz new file mode 100644 index 0000000..af01457 Binary files /dev/null and b/test_files/TOPAZ_IOD1_E001.fna.gz differ diff --git a/test_files/TOPAZ_RSS1_E007.fna.gz b/test_files/TOPAZ_RSS1_E007.fna.gz new file mode 100644 index 0000000..6120406 Binary files /dev/null and b/test_files/TOPAZ_RSS1_E007.fna.gz differ diff --git a/test_files/e.coli-o157.fasta.sketch b/test_files/e.coli-o157.fasta.sketch new file mode 100644 index 0000000..08b9240 Binary files /dev/null and b/test_files/e.coli-o157.fasta.sketch differ diff --git a/tests/integration_test.rs b/tests/integration_test.rs index cea45e9..10a2e1e 100644 --- a/tests/integration_test.rs +++ b/tests/integration_test.rs @@ -92,8 +92,39 @@ fn test_search() { let _af_r = out_line.split('\t').collect::>()[10] .parse::() .unwrap(); - assert!(ani > 0.97); - assert!(af_q > 0.80); + assert!(ani > 97.); + assert!(af_q > 80.); + + let mut cmd = Command::cargo_bin("skani").unwrap(); + let out = cmd + .arg("search") + .arg("-d") + .arg("./tests/results/test_sketch_dir/") + .arg("./test_files/e.coli-o157.fasta") + .arg("--median") + .arg("-n") + .arg("5") + .arg("--learned-ani") + .output(); + let out_line = std::str::from_utf8(&out.as_ref().unwrap().stdout).unwrap(); + println!("ANI search test learned"); + println!( + "{}", + std::str::from_utf8(&out.as_ref().unwrap().stdout).unwrap() + ); + let ani = out_line.split('\t').collect::>()[8] + .parse::() + .unwrap(); + let af_q = out_line.split('\t').collect::>()[9] + .parse::() + .unwrap(); + let _af_r = out_line.split('\t').collect::>()[10] + .parse::() + .unwrap(); + assert!(ani > 97.); + assert!(af_q > 80.); + + let mut cmd = Command::cargo_bin("skani").unwrap(); let assert = cmd @@ -162,9 +193,9 @@ fn test_search() { let af_r = out_line.split('\t').collect::>()[10] .parse::() .unwrap(); - assert!(ani > 0.70); + assert!(ani > 70.); //assert!(af_q > 0.80); - assert!(af_r > 0.50); + assert!(af_r > 30.); let err_line = std::str::from_utf8(&out.as_ref().unwrap().stderr).unwrap(); assert!(!err_line.contains("WARN") && !err_line.contains("ERROR")); @@ -194,9 +225,9 @@ fn test_dist() { let af_r = out_line.split('\t').collect::>()[10] .parse::() .unwrap(); - assert!(aai > 0.98); - assert!(af_q > 0.80); - assert!(af_r > 0.80); + assert!(aai > 98.); + assert!(af_q > 80.); + assert!(af_r > 80.); let mut cmd = Command::cargo_bin("skani").unwrap(); let out = cmd @@ -219,6 +250,31 @@ fn test_dist() { assert!(af_q > 90.); assert!(af_r > 90.); + let mut cmd = Command::cargo_bin("skani").unwrap(); + let out = cmd + .arg("dist") + .arg("./test_files/e.coli-EC590.fasta") + .arg("./test_files/e.coli-K12.fasta") + .arg("--marker-index") + .arg("-n") + .arg("3") + .arg("--learned-ani") + .output(); + let out_line = std::str::from_utf8(&out.as_ref().unwrap().stdout).unwrap(); + let ani = out_line.split('\t').collect::>()[8] + .parse::() + .unwrap(); + let af_q = out_line.split('\t').collect::>()[9] + .parse::() + .unwrap(); + let af_r = out_line.split('\t').collect::>()[10] + .parse::() + .unwrap(); + assert!(ani > 99.2); + assert!(ani < 100.); + assert!(af_q > 90.); + assert!(af_r > 90.); + let mut cmd = Command::cargo_bin("skani").unwrap(); let out = cmd .arg("dist") @@ -246,6 +302,57 @@ fn test_dist() { assert!(!err_line.contains("WARN") && !err_line.contains("ERROR")); + let mut cmd = Command::cargo_bin("skani").unwrap(); + let out = cmd + .arg("dist") + .arg("./test_files/e.coli-EC590.fasta") + .arg("./test_files/e.coli-K12.fasta") + .arg("--marker-index") + .arg("-n") + .arg("3") + .arg("--slow") + .output(); + let out_line = std::str::from_utf8(&out.as_ref().unwrap().stdout).unwrap(); + let ani = out_line.split('\t').collect::>()[8] + .parse::() + .unwrap(); + let af_q = out_line.split('\t').collect::>()[9] + .parse::() + .unwrap(); + let af_r = out_line.split('\t').collect::>()[10] + .parse::() + .unwrap(); + assert!(ani > 99.2); + assert!(ani < 100.); + assert!(af_q > 90.); + assert!(af_r > 90.); + + let mut cmd = Command::cargo_bin("skani").unwrap(); + let out = cmd + .arg("dist") + .arg("./test_files/e.coli-EC590.fasta") + .arg("./test_files/e.coli-K12.fasta") + .arg("--marker-index") + .arg("-n") + .arg("3") + .arg("--fast") + .output(); + let out_line = std::str::from_utf8(&out.as_ref().unwrap().stdout).unwrap(); + let ani = out_line.split('\t').collect::>()[8] + .parse::() + .unwrap(); + let af_q = out_line.split('\t').collect::>()[9] + .parse::() + .unwrap(); + let af_r = out_line.split('\t').collect::>()[10] + .parse::() + .unwrap(); + assert!(ani > 99.2); + assert!(ani < 100.); + assert!(af_q > 90.); + assert!(af_r > 90.); + + println!("ANI E.coli test"); println!( "{}", @@ -278,8 +385,8 @@ fn test_dist() { ); assert!(aai > 70.); assert!(aai < 85.); - assert!(af_q > 40.); - assert!(af_r > 40.); + assert!(af_q > 30.); + assert!(af_r > 30.); assert!(af_q < 90.); assert!(af_r < 90.); @@ -474,6 +581,19 @@ fn test_triangle() { .assert(); assert.success().code(0); + let mut cmd = Command::cargo_bin("skani").unwrap(); + let assert = cmd + .arg("triangle") + .arg("-l") + .arg("./test_files/query_list.txt") + .arg("-o") + .arg("./tests/results/output") + .arg("--learned-ani") + .assert(); + assert.success().code(0); + + + let mut cmd = Command::cargo_bin("skani").unwrap(); let out = cmd .arg("triangle") @@ -490,3 +610,4 @@ fn test_triangle() { assert!(!err_line.contains("WARN") && !err_line.contains("ERROR")); } + diff --git a/tests/tests.rs b/tests/tests.rs new file mode 100644 index 0000000..4dbd259 --- /dev/null +++ b/tests/tests.rs @@ -0,0 +1,152 @@ +use skani::chain::*; +use skani::seeding::*; +use skani::avx2_seeding::*; +use skani::regression::*; +use skani::file_io::*; +use skani::params::*; +use skani::types::*; +fn default_params(mode: Mode) -> (CommandParams, SketchParams) { + let cmd_params = CommandParams { + screen: false, + screen_val: 0.00, + mode: mode, + out_file_name: "".to_string(), + ref_files: vec![], + query_files: vec![], + refs_are_sketch: false, + queries_are_sketch: false, + robust: false, + median: false, + sparse: false, + full_matrix: false, + max_results: 10000000, + individual_contig_q: false, + individual_contig_r: false, + min_aligned_frac: 0.15, + keep_refs: false, + est_ci: false, + learned_ani: true, + learned_ani_cmd: false, + detailed_out: false, + }; + + let sketch_params = SketchParams::new(1000, 125, 15, false, false); + return (cmd_params, sketch_params); +} + +#[test] +fn code_ecoli_test_simple() { + let (mut command_params, sketch_params) = default_params(Mode::Dist); + command_params + .ref_files + .push("./test_files/e.coli-W.fasta.gz".to_string()); + command_params + .query_files + .push("./test_files/e.coli-W.fasta.gz".to_string()); + + let ref_sketch = fastx_to_sketches(&command_params.ref_files, &sketch_params, true)[0].clone(); + let query_sketch = + fastx_to_sketches(&command_params.query_files, &sketch_params, true)[0].clone(); + let map_params = map_params_from_sketch(&ref_sketch, sketch_params.use_aa, &command_params); + let ani_res = chain_seeds(&ref_sketch, &query_sketch, map_params); + assert!(ani_res.ani >= 1.0); + assert!(ani_res.align_fraction_query >= 0.99); + assert!(ani_res.align_fraction_ref >= 0.99); +} + +#[test] +fn code_ecoli_plasmid_test() { + let (mut command_params, sketch_params) = default_params(Mode::Dist); + command_params + .ref_files + .push("./test_files/e.coli-o157.fasta.sketch".to_string()); + command_params + .query_files + .push("./test_files/o157_plasmid.fasta".to_string()); + + let ref_sketch = sketches_from_sketch(&command_params.ref_files).1[0].clone(); + let query_sketch = + fastx_to_sketches(&command_params.query_files, &sketch_params, true)[0].clone(); + let map_params = map_params_from_sketch(&ref_sketch, sketch_params.use_aa, &command_params); + let ani_res = chain_seeds(&ref_sketch, &query_sketch, map_params); + assert!(ani_res.ani >= 1.0); + assert!(ani_res.align_fraction_query >= 0.99); + assert!(ani_res.align_fraction_ref >= 0.005); +} + +#[test] +fn code_eukaryote_test() { + +/* Mummer stats + [Bases] + TotalBases 37074820 45684866 + AlignedBases 28626642(77.2132%) 28594130(62.5899%) + UnalignedBases 8448178(22.7868%) 17090736(37.4101%) + + [Alignments] + 1-to-1 10157 10157 + TotalLength 28580162 28584588 + AvgLength 2813.8389 2814.2747 + AvgIdentity 98.6310 98.6310 +*/ + + let (mut command_params, sketch_params) = default_params(Mode::Dist); + command_params + .ref_files + .push("./test_files/TOPAZ_IOD1_E001.fna.gz".to_string()); + command_params + .query_files + .push("./test_files/TOPAZ_RSS1_E007.fna.gz".to_string()); + + let ref_sketch = fastx_to_sketches(&command_params.ref_files, &sketch_params, true)[0].clone(); + let query_sketch = + fastx_to_sketches(&command_params.query_files, &sketch_params, true)[0].clone(); + let map_params = map_params_from_sketch(&ref_sketch, sketch_params.use_aa, &command_params); + let mut ani_res = chain_seeds(&ref_sketch, &query_sketch, map_params); + + assert!(ani_res.ani >= 0.98); + assert!(ani_res.align_fraction_ref>= 0.70); + assert!(ani_res.align_fraction_query >= 0.55); + + assert!(ani_res.align_fraction_ref<= 0.80); + assert!(ani_res.align_fraction_query <= 0.65); + let old_ani = ani_res.ani; + + let model_opt = get_model(sketch_params.c, command_params.learned_ani); + if model_opt.is_some(){ + let model = model_opt.as_ref().unwrap(); + predict_from_ani_res(&mut ani_res, &model); + } + assert!(ani_res.ani >= 0.98); + assert!(ani_res.ani <= old_ani); + println!("{:?}", ani_res); +} + +#[test] +fn avx2_vs_normal_code(){ + let str1 = b"ATCAGATTTAAAAAAAAATTTTGCTAGCTGATCGATCGATCGATGTGTATATATTAAAAGAGAGAGAGGGGGGGGAAAAAAAAAAAAACTGATCGATCGATGCTAGCTAGTCAGTCGATG"; + let (mut command_params, mut sketch_params) = default_params(Mode::Dist); + sketch_params.c = 10; + let mut new_sketch1 = Sketch::default(); + let mut new_sketch2 = Sketch::default(); + unsafe{ + avx2_fmh_seeds(str1, &sketch_params, 0, &mut new_sketch1, true); + } + + fmh_seeds(str1, &sketch_params, 0, &mut new_sketch2, true); + assert!(new_sketch1 == new_sketch2); + //println!("{:?}", new_sketch1.kmer_seeds_k.unwrap()); +} + + +//Ns are treated as As right now. Luckily, the hash function doesn't accept AAAAAA... +//for FMH when c = 30. +#[test] +fn NNN_test_code(){ + let str1 = b"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNn"; + let (mut command_params, mut sketch_params) = default_params(Mode::Dist); + sketch_params.c = 30; + let mut new_sketch1 = Sketch::default(); + fmh_seeds(str1, &sketch_params, 0, &mut new_sketch1, true); + assert!(new_sketch1.kmer_seeds_k.unwrap().len() == 0); +}