[INFO] cloning repository https://github.com/Jakeelamb/Raptor [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/Jakeelamb/Raptor" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJakeelamb%2FRaptor", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJakeelamb%2FRaptor'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 2817d46538ee1172cac1e57b10357c4d468ea01d [INFO] checking Jakeelamb/Raptor against master#9c3064e131f4939cc95a29bb11413c49bbda1491 for pr-144098 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJakeelamb%2FRaptor" "/workspace/builds/worker-2-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc2/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/Jakeelamb/Raptor [INFO] finished tweaking git repo https://github.com/Jakeelamb/Raptor [INFO] tweaked toml for git repo https://github.com/Jakeelamb/Raptor written to /workspace/builds/worker-2-tc2/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/Jakeelamb/Raptor on toolchain 9c3064e131f4939cc95a29bb11413c49bbda1491 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+9c3064e131f4939cc95a29bb11413c49bbda1491" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/Jakeelamb/Raptor already has a lockfile, it will not be regenerated [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+9c3064e131f4939cc95a29bb11413c49bbda1491" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:cf8efcab8866f2cf4285301c7418e2f4f2a9b088c91ba69c40d5b659f81557f7" "/opt/rustwide/cargo-home/bin/cargo" "+9c3064e131f4939cc95a29bb11413c49bbda1491" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 60c48d165c230c263c89d5770f0fdd9274a977cdcdcbbbdb8a69169264ea8b74 [INFO] running `Command { std: "docker" "start" "-a" "60c48d165c230c263c89d5770f0fdd9274a977cdcdcbbbdb8a69169264ea8b74", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "60c48d165c230c263c89d5770f0fdd9274a977cdcdcbbbdb8a69169264ea8b74", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "60c48d165c230c263c89d5770f0fdd9274a977cdcdcbbbdb8a69169264ea8b74", kill_on_drop: false }` [INFO] [stdout] 60c48d165c230c263c89d5770f0fdd9274a977cdcdcbbbdb8a69169264ea8b74 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:cf8efcab8866f2cf4285301c7418e2f4f2a9b088c91ba69c40d5b659f81557f7" "/opt/rustwide/cargo-home/bin/cargo" "+9c3064e131f4939cc95a29bb11413c49bbda1491" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 66fc035fe69e2123649556b7168890ba4d9ba24a61ad8b8fbab316ae97cc08e7 [INFO] running `Command { std: "docker" "start" "-a" "66fc035fe69e2123649556b7168890ba4d9ba24a61ad8b8fbab316ae97cc08e7", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.94 [INFO] [stderr] Compiling unicode-ident v1.0.18 [INFO] [stderr] Compiling libc v0.2.171 [INFO] [stderr] Compiling pkg-config v0.3.32 [INFO] [stderr] Checking memchr v2.7.4 [INFO] [stderr] Checking once_cell v1.21.3 [INFO] [stderr] Compiling glob v0.3.2 [INFO] [stderr] Compiling prettyplease v0.2.31 [INFO] [stderr] Compiling semver v1.0.26 [INFO] [stderr] Compiling rustix v0.38.44 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling cc v1.2.18 [INFO] [stderr] Compiling bitflags v2.9.0 [INFO] [stderr] Compiling linux-raw-sys v0.4.15 [INFO] [stderr] Compiling either v1.15.0 [INFO] [stderr] Compiling regex-syntax v0.8.5 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling libloading v0.8.6 [INFO] [stderr] Compiling matrixmultiply v0.3.9 [INFO] [stderr] Compiling shell-words v1.1.0 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling bindgen v0.69.5 [INFO] [stderr] Compiling home v0.5.11 [INFO] [stderr] Compiling build-probe-mpi v0.1.4 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Checking log v0.4.27 [INFO] [stderr] Compiling rustc_version v0.4.1 [INFO] [stderr] Checking ryu v1.0.20 [INFO] [stderr] Checking aho-corasick v1.1.3 [INFO] [stderr] Compiling lazycell v1.3.0 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling lazy_static v1.5.0 [INFO] [stderr] Compiling rustversion v1.0.20 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling yeslogic-fontconfig-sys v6.0.0 [INFO] [stderr] Compiling quote v1.0.40 [INFO] [stderr] Compiling pathfinder_simd v0.5.4 [INFO] [stderr] Checking miniz_oxide v0.8.7 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Checking num-integer v0.1.46 [INFO] [stderr] Checking num-complex v0.4.6 [INFO] [stderr] Checking approx v0.5.1 [INFO] [stderr] Compiling typenum v1.18.0 [INFO] [stderr] Compiling syn v2.0.100 [INFO] [stderr] Checking getrandom v0.2.15 [INFO] [stderr] Checking flate2 v1.1.1 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking num-bigint v0.4.6 [INFO] [stderr] Checking rand_core 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[stderr] Checking zerocopy v0.7.35 [INFO] [stderr] Checking editdistancek v1.0.2 [INFO] [stderr] Checking fixedbitset v0.5.7 [INFO] [stderr] Checking triple_accel v0.4.0 [INFO] [stderr] Checking cfg-if v0.1.10 [INFO] [stderr] Checking strum v0.25.0 [INFO] [stderr] Checking seahash v3.0.7 [INFO] [stderr] Checking humantime v2.2.0 [INFO] [stderr] Checking bytecount v0.6.8 [INFO] [stderr] Checking petgraph v0.7.1 [INFO] [stderr] Checking env_logger v0.10.2 [INFO] [stderr] Checking crossbeam v0.8.4 [INFO] [stderr] Checking tracing-subscriber v0.3.19 [INFO] [stderr] Checking rayon v1.10.0 [INFO] [stderr] Checking ndarray-stats v0.5.1 [INFO] [stderr] Checking smartcore v0.3.2 [INFO] [stderr] Checking num_cpus v1.16.0 [INFO] [stderr] Checking tempfile v3.19.1 [INFO] [stderr] Compiling serde_derive v1.0.219 [INFO] [stderr] Compiling bytemuck_derive v1.9.3 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling tracing-attributes v0.1.28 [INFO] [stderr] Compiling clap_derive v4.5.32 [INFO] [stderr] Compiling strum_macros v0.25.3 [INFO] [stderr] Checking enum-map v2.7.3 [INFO] [stderr] Checking bytemuck v1.22.0 [INFO] [stderr] Checking thiserror v1.0.69 [INFO] [stderr] Checking image v0.24.9 [INFO] [stderr] Checking safe_arch v0.7.4 [INFO] [stderr] Checking fasthash v0.4.0 [INFO] [stderr] Checking gfa v0.10.1 [INFO] [stderr] Checking tracing v0.1.41 [INFO] [stderr] Checking nalgebra v0.27.1 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Checking wide v0.7.32 [INFO] [stderr] Checking clap v4.5.35 [INFO] [stderr] Checking serde v1.0.219 [INFO] [stderr] Checking plotters-bitmap v0.3.7 [INFO] [stderr] Checking plotters v0.3.7 [INFO] [stderr] Checking csv v1.3.1 [INFO] [stderr] Checking multimap v0.9.1 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Compiling mpi-sys v0.2.2 [INFO] [stderr] Checking libffi v3.2.0 [INFO] [stderr] Checking statrs v0.15.0 [INFO] [stderr] Checking bio v1.6.0 [INFO] [stderr] Checking raptor v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/graph/assembler.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ndarray_stats::QuantileExt` [INFO] [stdout] --> src/visualize/pca.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use ndarray_stats::QuantileExt; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ndarray_stats::QuantileExt` [INFO] [stdout] --> src/visualize/pca.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use ndarray_stats::QuantileExt; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/graph/assembler.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `contigs` [INFO] [stdout] --> src/graph/partition.rs:99:5 [INFO] [stdout] | [INFO] [stdout] 99 | contigs: &[String] [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_contigs` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `contigs` [INFO] [stdout] --> src/graph/partition.rs:99:5 [INFO] [stdout] | [INFO] [stdout] 99 | contigs: &[String] [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_contigs` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `k` is never read [INFO] [stdout] --> src/pipeline/assemble.rs:88:13 [INFO] [stdout] | [INFO] [stdout] 88 | let mut k = 31; // Default k-mer size [INFO] [stdout] | ^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `k` is never read [INFO] [stdout] --> src/pipeline/assemble.rs:88:13 [INFO] [stdout] | [INFO] [stdout] 88 | let mut k = 31; // Default k-mer size [INFO] [stdout] | ^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output_gfa` [INFO] [stdout] --> src/pipeline/assemble.rs:549:5 [INFO] [stdout] | [INFO] [stdout] 549 | output_gfa: bool, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_gfa` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `adaptive_k` [INFO] [stdout] --> src/pipeline/assemble.rs:550:5 [INFO] [stdout] | [INFO] [stdout] 550 | adaptive_k: bool, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_adaptive_k` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `use_rle` [INFO] [stdout] --> src/pipeline/assemble.rs:551:5 [INFO] [stdout] | [INFO] [stdout] 551 | use_rle: bool, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_use_rle` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:47:5 [INFO] [stdout] | [INFO] [stdout] 47 | output_path: &str, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `gtf_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:48:5 [INFO] [stdout] | [INFO] [stdout] 48 | gtf_path: Option<&str>, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gtf_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_tpm` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:51:5 [INFO] [stdout] | [INFO] [stdout] 51 | min_tpm: Option, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_tpm` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `strand_aware` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:52:5 [INFO] [stdout] | [INFO] [stdout] 52 | strand_aware: bool, [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand_aware` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bam_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:53:5 [INFO] [stdout] | [INFO] [stdout] 53 | bam_path: Option<&str>, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bam_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `long_reads` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:54:5 [INFO] [stdout] | [INFO] [stdout] 54 | long_reads: Option<&str>, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_long_reads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `get_output_filename` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:55:5 [INFO] [stdout] | [INFO] [stdout] 55 | get_output_filename: fn(&str, Option<&str>) -> String, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_get_output_filename` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output_gfa` [INFO] [stdout] --> src/pipeline/assemble.rs:549:5 [INFO] [stdout] | [INFO] [stdout] 549 | output_gfa: bool, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_gfa` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `adaptive_k` [INFO] [stdout] --> src/pipeline/assemble.rs:550:5 [INFO] [stdout] | [INFO] [stdout] 550 | adaptive_k: bool, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_adaptive_k` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `use_rle` [INFO] [stdout] --> src/pipeline/assemble.rs:551:5 [INFO] [stdout] | [INFO] [stdout] 551 | use_rle: bool, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_use_rle` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `csv_path` [INFO] [stdout] --> src/quant/align_counts.rs:135:27 [INFO] [stdout] | [INFO] [stdout] 135 | pub fn load_counts_matrix(csv_path: &str, transcripts: &[Transcript]) -> Result>> { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_csv_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:47:5 [INFO] [stdout] | [INFO] [stdout] 47 | output_path: &str, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `gtf_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:48:5 [INFO] [stdout] | [INFO] [stdout] 48 | gtf_path: Option<&str>, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gtf_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_tpm` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:51:5 [INFO] [stdout] | [INFO] [stdout] 51 | min_tpm: Option, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_tpm` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `strand_aware` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:52:5 [INFO] [stdout] | [INFO] [stdout] 52 | strand_aware: bool, [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand_aware` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bam_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:53:5 [INFO] [stdout] | [INFO] [stdout] 53 | bam_path: Option<&str>, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bam_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `long_reads` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:54:5 [INFO] [stdout] | [INFO] [stdout] 54 | long_reads: Option<&str>, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_long_reads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `get_output_filename` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:55:5 [INFO] [stdout] | [INFO] [stdout] 55 | get_output_filename: fn(&str, Option<&str>) -> String, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_get_output_filename` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `csv_path` [INFO] [stdout] --> src/quant/align_counts.rs:135:27 [INFO] [stdout] | [INFO] [stdout] 135 | pub fn load_counts_matrix(csv_path: &str, transcripts: &[Transcript]) -> Result>> { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_csv_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `median` is never used [INFO] [stdout] --> src/kmer/normalize.rs:105:4 [INFO] [stdout] | [INFO] [stdout] 105 | fn median(values: &mut [u16]) -> u16 { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_path_confidence` is never used [INFO] [stdout] --> src/graph/isoform_parallel.rs:106:4 [INFO] [stdout] | [INFO] [stdout] 106 | fn calculate_path_confidence(graph: &IsoformGraph, path: &[usize]) -> f32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `capacity` is never read [INFO] [stdout] --> src/accel/gpu.rs:10:9 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct GpuKmerCounter { [INFO] [stdout] | -------------- field in this struct [INFO] [stdout] 9 | width: usize, [INFO] [stdout] 10 | capacity: usize, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `create_test_contigs` is never used [INFO] [stdout] --> src/io/metadata.rs:112:8 [INFO] [stdout] | [INFO] [stdout] 112 | fn create_test_contigs() -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `median` is never used [INFO] [stdout] --> src/kmer/normalize.rs:105:4 [INFO] [stdout] | [INFO] [stdout] 105 | fn median(values: &mut [u16]) -> u16 { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_path_confidence` is never used [INFO] [stdout] --> src/graph/isoform_parallel.rs:106:4 [INFO] [stdout] | [INFO] [stdout] 106 | fn calculate_path_confidence(graph: &IsoformGraph, path: &[usize]) -> f32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `capacity` is never read [INFO] [stdout] --> src/accel/gpu.rs:10:9 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct GpuKmerCounter { [INFO] [stdout] | -------------- field in this struct [INFO] [stdout] 9 | width: usize, [INFO] [stdout] 10 | capacity: usize, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `self` [INFO] [stdout] --> examples/traverse_paths.rs:4:15 [INFO] [stdout] | [INFO] [stdout] 4 | use std::io::{self, BufWriter, Write}; [INFO] [stdout] | ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `i` [INFO] [stdout] --> examples/traverse_paths.rs:91:14 [INFO] [stdout] | [INFO] [stdout] 91 | for (i, (seg_id, orientation)) in path.iter().enumerate() { [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_i` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `DEFAULT_MAX_READS` is never used [INFO] [stdout] --> src/bin/normalize_paired_reads.rs:11:7 [INFO] [stdout] | [INFO] [stdout] 11 | const DEFAULT_MAX_READS: usize = 5_000_000; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::time::Instant` [INFO] [stdout] --> src/bin/count_gpu.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use std::time::Instant; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `k` [INFO] [stdout] --> src/bin/count_gpu.rs:8:9 [INFO] [stdout] | [INFO] [stdout] 8 | let k = 25; [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_k` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `sequences` [INFO] [stdout] --> src/bin/count_gpu.rs:12:9 [INFO] [stdout] | [INFO] [stdout] 12 | let sequences: Vec = records.iter().map(|r| r.sequence.clone()).collect(); [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sequences` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::time::Instant` [INFO] [stdout] --> src/bin/count_gpu.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use std::time::Instant; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `k` [INFO] [stdout] --> src/bin/count_gpu.rs:8:9 [INFO] [stdout] | [INFO] [stdout] 8 | let k = 25; [INFO] [stdout] | ^ help: if this is intentional, prefix it with an underscore: `_k` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `sequences` [INFO] [stdout] --> src/bin/count_gpu.rs:12:9 [INFO] [stdout] | [INFO] [stdout] 12 | let sequences: Vec = records.iter().map(|r| r.sequence.clone()).collect(); [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_sequences` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `count` [INFO] [stdout] --> src/bin/assemble.rs:142:17 [INFO] [stdout] | [INFO] [stdout] 142 | for (kmer, &count) in sorted_kmers { [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_count` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `count` [INFO] [stdout] --> src/bin/assemble.rs:142:17 [INFO] [stdout] | [INFO] [stdout] 142 | for (kmer, &count) in sorted_kmers { [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_count` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: constant `DEFAULT_MAX_READS` is never used [INFO] [stdout] --> src/bin/normalize_paired_reads.rs:11:7 [INFO] [stdout] | [INFO] [stdout] 11 | const DEFAULT_MAX_READS: usize = 5_000_000; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/graph/assembler.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ndarray_stats::QuantileExt` [INFO] [stdout] --> src/visualize/pca.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use ndarray_stats::QuantileExt; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `rayon::prelude` [INFO] [stdout] --> src/graph/assembler.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use rayon::prelude::*; [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ndarray_stats::QuantileExt` [INFO] [stdout] --> src/visualize/pca.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use ndarray_stats::QuantileExt; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `contigs` [INFO] [stdout] --> src/graph/partition.rs:99:5 [INFO] [stdout] | [INFO] [stdout] 99 | contigs: &[String] [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_contigs` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `contigs` [INFO] [stdout] --> src/graph/partition.rs:99:5 [INFO] [stdout] | [INFO] [stdout] 99 | contigs: &[String] [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_contigs` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `k` is never read [INFO] [stdout] --> src/pipeline/assemble.rs:88:13 [INFO] [stdout] | [INFO] [stdout] 88 | let mut k = 31; // Default k-mer size [INFO] [stdout] | ^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `k` is never read [INFO] [stdout] --> src/pipeline/assemble.rs:88:13 [INFO] [stdout] | [INFO] [stdout] 88 | let mut k = 31; // Default k-mer size [INFO] [stdout] | ^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output_gfa` [INFO] [stdout] --> src/pipeline/assemble.rs:549:5 [INFO] [stdout] | [INFO] [stdout] 549 | output_gfa: bool, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_gfa` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `adaptive_k` [INFO] [stdout] --> src/pipeline/assemble.rs:550:5 [INFO] [stdout] | [INFO] [stdout] 550 | adaptive_k: bool, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_adaptive_k` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `use_rle` [INFO] [stdout] --> src/pipeline/assemble.rs:551:5 [INFO] [stdout] | [INFO] [stdout] 551 | use_rle: bool, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_use_rle` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:47:5 [INFO] [stdout] | [INFO] [stdout] 47 | output_path: &str, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `gtf_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:48:5 [INFO] [stdout] | [INFO] [stdout] 48 | gtf_path: Option<&str>, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gtf_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_tpm` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:51:5 [INFO] [stdout] | [INFO] [stdout] 51 | min_tpm: Option, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_tpm` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `strand_aware` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:52:5 [INFO] [stdout] | [INFO] [stdout] 52 | strand_aware: bool, [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand_aware` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bam_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:53:5 [INFO] [stdout] | [INFO] [stdout] 53 | bam_path: Option<&str>, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bam_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `long_reads` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:54:5 [INFO] [stdout] | [INFO] [stdout] 54 | long_reads: Option<&str>, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_long_reads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `get_output_filename` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:55:5 [INFO] [stdout] | [INFO] [stdout] 55 | get_output_filename: fn(&str, Option<&str>) -> String, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_get_output_filename` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `csv_path` [INFO] [stdout] --> src/quant/align_counts.rs:135:27 [INFO] [stdout] | [INFO] [stdout] 135 | pub fn load_counts_matrix(csv_path: &str, transcripts: &[Transcript]) -> Result>> { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_csv_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output_gfa` [INFO] [stdout] --> src/pipeline/assemble.rs:549:5 [INFO] [stdout] | [INFO] [stdout] 549 | output_gfa: bool, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_gfa` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `adaptive_k` [INFO] [stdout] --> src/pipeline/assemble.rs:550:5 [INFO] [stdout] | [INFO] [stdout] 550 | adaptive_k: bool, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_adaptive_k` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `use_rle` [INFO] [stdout] --> src/pipeline/assemble.rs:551:5 [INFO] [stdout] | [INFO] [stdout] 551 | use_rle: bool, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_use_rle` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:47:5 [INFO] [stdout] | [INFO] [stdout] 47 | output_path: &str, [INFO] [stdout] | ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_output_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `gtf_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:48:5 [INFO] [stdout] | [INFO] [stdout] 48 | gtf_path: Option<&str>, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gtf_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_tpm` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:51:5 [INFO] [stdout] | [INFO] [stdout] 51 | min_tpm: Option, [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_min_tpm` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `strand_aware` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:52:5 [INFO] [stdout] | [INFO] [stdout] 52 | strand_aware: bool, [INFO] [stdout] | ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_strand_aware` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `bam_path` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:53:5 [INFO] [stdout] | [INFO] [stdout] 53 | bam_path: Option<&str>, [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_bam_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `long_reads` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:54:5 [INFO] [stdout] | [INFO] [stdout] 54 | long_reads: Option<&str>, [INFO] [stdout] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_long_reads` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `get_output_filename` [INFO] [stdout] --> src/pipeline/isoform_processor.rs:55:5 [INFO] [stdout] | [INFO] [stdout] 55 | get_output_filename: fn(&str, Option<&str>) -> String, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_get_output_filename` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `threads` [INFO] [stdout] --> src/main.rs:38:13 [INFO] [stdout] | [INFO] [stdout] 38 | threads, [INFO] [stdout] | ^^^^^^^ help: try ignoring the field: `threads: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `coverage_target` [INFO] [stdout] --> src/main.rs:40:13 [INFO] [stdout] | [INFO] [stdout] 40 | coverage_target, [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: try ignoring the field: `coverage_target: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `max_reads` [INFO] [stdout] --> src/main.rs:41:13 [INFO] [stdout] | [INFO] [stdout] 41 | max_reads [INFO] [stdout] | ^^^^^^^^^ help: try ignoring the field: `max_reads: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `threads` [INFO] [stdout] --> src/main.rs:62:13 [INFO] [stdout] | [INFO] [stdout] 62 | threads, [INFO] [stdout] | ^^^^^^^ help: try ignoring the field: `threads: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `distributed` [INFO] [stdout] --> src/main.rs:66:13 [INFO] [stdout] | [INFO] [stdout] 66 | distributed, [INFO] [stdout] | ^^^^^^^^^^^ help: try ignoring the field: `distributed: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `buckets` [INFO] [stdout] --> src/main.rs:67:13 [INFO] [stdout] | [INFO] [stdout] 67 | buckets, [INFO] [stdout] | ^^^^^^^ help: try ignoring the field: `buckets: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_path_len` [INFO] [stdout] --> src/main.rs:83:13 [INFO] [stdout] | [INFO] [stdout] 83 | min_path_len, [INFO] [stdout] | ^^^^^^^^^^^^ help: try ignoring the field: `min_path_len: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `dev_mode` [INFO] [stdout] --> src/main.rs:84:13 [INFO] [stdout] | [INFO] [stdout] 84 | dev_mode, [INFO] [stdout] | ^^^^^^^^ help: try ignoring the field: `dev_mode: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output` [INFO] [stdout] --> src/main.rs:437:39 [INFO] [stdout] | [INFO] [stdout] 437 | Commands::Visualize { matrix, output, heatmap, pca, components } => { [INFO] [stdout] | ^^^^^^ help: try ignoring the field: `output: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `csv_path` [INFO] [stdout] --> src/quant/align_counts.rs:135:27 [INFO] [stdout] | [INFO] [stdout] 135 | pub fn load_counts_matrix(csv_path: &str, transcripts: &[Transcript]) -> Result>> { [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_csv_path` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait `Log2` is never used [INFO] [stdout] --> src/main.rs:278:19 [INFO] [stdout] | [INFO] [stdout] 278 | trait Log2 { [INFO] [stdout] | ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `read_long_reads` is never used [INFO] [stdout] --> src/io/fastq.rs:180:8 [INFO] [stdout] | [INFO] [stdout] 180 | pub fn read_long_reads(path: &str) -> io::Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `write_record` is never used [INFO] [stdout] --> src/io/fasta.rs:37:12 [INFO] [stdout] | [INFO] [stdout] 26 | impl FastaWriter { [INFO] [stdout] | ---------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 37 | pub fn write_record(&mut self, header: &str, sequence: &str) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `write_paths` is never used [INFO] [stdout] --> src/io/gfa.rs:40:12 [INFO] [stdout] | [INFO] [stdout] 12 | impl GfaWriter { [INFO] [stdout] | -------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 40 | pub fn write_paths(&mut self, contigs: &[Contig]) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `with_coverage` is never used [INFO] [stdout] --> src/io/gfa2.rs:25:12 [INFO] [stdout] | [INFO] [stdout] 14 | impl Gfa2Writer { [INFO] [stdout] | --------------- associated function in this implementation [INFO] [stdout] ... [INFO] [stdout] 25 | pub fn with_coverage(path: &str, coverage: HashMap) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `write_detailed_gff3` is never used [INFO] [stdout] --> src/io/gff3.rs:45:8 [INFO] [stdout] | [INFO] [stdout] 45 | pub fn write_detailed_gff3( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `write_detailed_gtf` is never used [INFO] [stdout] --> src/io/gtf.rs:70:8 [INFO] [stdout] | [INFO] [stdout] 70 | pub fn write_detailed_gtf( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `filter_nanopore_reads` is never used [INFO] [stdout] --> src/io/longread.rs:5:8 [INFO] [stdout] | [INFO] [stdout] 5 | pub fn filter_nanopore_reads(reads: &[FastqRecord], min_len: usize) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `align_long_reads` is never used [INFO] [stdout] --> src/io/longread.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 14 | pub fn align_long_reads(contig: &str, long_reads: &[FastqRecord]) -> Vec<(usize, usize)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_exact_position` is never used [INFO] [stdout] --> src/io/longread.rs:46:4 [INFO] [stdout] | [INFO] [stdout] 46 | fn find_exact_position(contig: &str, read: &str, approximate_start: usize) -> Option { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `integrate_long_reads_for_polishing` is never used [INFO] [stdout] --> src/io/longread.rs:55:8 [INFO] [stdout] | [INFO] [stdout] 55 | pub fn integrate_long_reads_for_polishing( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `OdgiNode` is never constructed [INFO] [stdout] --> src/io/odgi.rs:9:8 [INFO] [stdout] | [INFO] [stdout] 9 | struct OdgiNode { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `OdgiPath` is never constructed [INFO] [stdout] --> src/io/odgi.rs:16:8 [INFO] [stdout] | [INFO] [stdout] 16 | struct OdgiPath { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `OdgiGraph` is never constructed [INFO] [stdout] --> src/io/odgi.rs:23:8 [INFO] [stdout] | [INFO] [stdout] 23 | struct OdgiGraph { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `export_odgi_json` is never used [INFO] [stdout] --> src/io/odgi.rs:30:8 [INFO] [stdout] | [INFO] [stdout] 30 | pub fn export_odgi_json( [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `export_path_metadata_json` is never used [INFO] [stdout] --> src/io/odgi.rs:128:8 [INFO] [stdout] | [INFO] [stdout] 128 | pub fn export_path_metadata_json( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `export_paths_to_fasta` is never used [INFO] [stdout] --> src/io/export.rs:8:8 [INFO] [stdout] | [INFO] [stdout] 8 | pub fn export_paths_to_fasta( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `export_path_metadata` is never used [INFO] [stdout] --> src/io/export.rs:31:8 [INFO] [stdout] | [INFO] [stdout] 31 | pub fn export_path_metadata( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `export_odgi_paths` is never used [INFO] [stdout] --> src/io/export.rs:61:8 [INFO] [stdout] | [INFO] [stdout] 61 | pub fn export_odgi_paths( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `export_dot_graph` is never used [INFO] [stdout] --> src/io/export.rs:82:8 [INFO] [stdout] | [INFO] [stdout] 82 | pub fn export_dot_graph( [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `write_transcript_json` is never used [INFO] [stdout] --> src/io/transcript_io.rs:156:8 [INFO] [stdout] | [INFO] [stdout] 156 | pub fn write_transcript_json(path: &str, transcripts: &[Transcript]) -> io::Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `rle_decode` is never used [INFO] [stdout] --> src/kmer/rle.rs:23:8 [INFO] [stdout] | [INFO] [stdout] 23 | pub fn rle_decode(encoded: &[(u8, u8)]) -> String { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type alias `Kmer` is never used [INFO] [stdout] --> src/kmer/kmer.rs:1:10 [INFO] [stdout] | [INFO] [stdout] 1 | pub type Kmer = String; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `encode_kmer` is never used [INFO] [stdout] --> src/kmer/kmer.rs:4:8 [INFO] [stdout] | [INFO] [stdout] 4 | pub fn encode_kmer(seq: &str) -> Option { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `AbundanceStats` is never constructed [INFO] [stdout] --> src/kmer/normalize.rs:8:12 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct AbundanceStats { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `estimate_read_abundance` is never used [INFO] [stdout] --> src/kmer/normalize.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 14 | pub fn estimate_read_abundance(seq: &str, k: usize, sketch: &[u32]) -> AbundanceStats { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `median` is never used [INFO] [stdout] --> src/kmer/normalize.rs:105:4 [INFO] [stdout] | [INFO] [stdout] 105 | fn median(values: &mut [u16]) -> u16 { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `detect_rle_repeats` is never used [INFO] [stdout] --> src/kmer/repeat.rs:4:8 [INFO] [stdout] | [INFO] [stdout] 4 | pub fn detect_rle_repeats(seq: &str, min_len: usize, min_unit: usize) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_repeat_positions` is never used [INFO] [stdout] --> src/kmer/repeat.rs:28:8 [INFO] [stdout] | [INFO] [stdout] 28 | pub fn find_repeat_positions(seq: &str, pattern: &str, min_len: usize) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `collapse_repeats` is never used [INFO] [stdout] --> src/kmer/repeat.rs:53:8 [INFO] [stdout] | [INFO] [stdout] 53 | pub fn collapse_repeats(seq: &str, min_length: usize) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `kmer_path` is never read [INFO] [stdout] --> src/graph/assembler.rs:10:9 [INFO] [stdout] | [INFO] [stdout] 7 | pub struct Contig { [INFO] [stdout] | ------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 10 | pub kmer_path: Vec, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Contig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `to_rle` is never used [INFO] [stdout] --> src/graph/assembler.rs:15:12 [INFO] [stdout] | [INFO] [stdout] 13 | impl Contig { [INFO] [stdout] | ----------- method in this implementation [INFO] [stdout] 14 | /// Convert the contig sequence to run-length encoding [INFO] [stdout] 15 | pub fn to_rle(&self) -> Vec<(u8, u8)> { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `distance` and `shift` are never read [INFO] [stdout] --> src/graph/stitch.rs:153:9 [INFO] [stdout] | [INFO] [stdout] 151 | pub struct OverlapInfo { [INFO] [stdout] | ----------- fields in this struct [INFO] [stdout] 152 | pub overlap_length: usize, [INFO] [stdout] 153 | pub distance: usize, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] 154 | pub shift: usize, [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `OverlapInfo` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_paths_from_gfa` is never used [INFO] [stdout] --> src/graph/stitch.rs:158:8 [INFO] [stdout] | [INFO] [stdout] 158 | pub fn load_paths_from_gfa(gfa_path: &str) -> Result, std::io::Error> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `cluster_contigs` is never used [INFO] [stdout] --> src/graph/partition.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 14 | pub fn cluster_contigs(graph: &DiGraphMap) -> HashMap> { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `merge_small_clusters` is never used [INFO] [stdout] --> src/graph/partition.rs:46:8 [INFO] [stdout] | [INFO] [stdout] 46 | pub fn merge_small_clusters( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_cluster_similarity` is never used [INFO] [stdout] --> src/graph/partition.rs:96:4 [INFO] [stdout] | [INFO] [stdout] 96 | fn calculate_cluster_similarity( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `merge_clusters` is never used [INFO] [stdout] --> src/graph/partition.rs:117:8 [INFO] [stdout] | [INFO] [stdout] 117 | pub fn merge_clusters(clusters: Vec>, _distance_matrix: &[Vec], _contigs: &[String]) -> Vec> { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compute_edge_weight` is never used [INFO] [stdout] --> src/graph/edge_weight.rs:15:8 [INFO] [stdout] | [INFO] [stdout] 15 | pub fn compute_edge_weight(from: usize, to: usize, coverage: &[f32], pair_support: usize) -> f32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `PairLinkTracker` is never constructed [INFO] [stdout] --> src/graph/edge_weight.rs:31:12 [INFO] [stdout] | [INFO] [stdout] 31 | pub struct PairLinkTracker { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new`, `add_pair_link`, `get_pair_support`, and `get_all_pair_links` are never used [INFO] [stdout] --> src/graph/edge_weight.rs:38:12 [INFO] [stdout] | [INFO] [stdout] 36 | impl PairLinkTracker { [INFO] [stdout] | -------------------- associated items in this implementation [INFO] [stdout] 37 | /// Create a new PairLinkTracker [INFO] [stdout] 38 | pub fn new() -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 45 | pub fn add_pair_link(&mut self, from: usize, to: usize) { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 50 | pub fn get_pair_support(&self, from: usize, to: usize) -> usize { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 55 | pub fn get_all_pair_links(&self) -> &HashMap<(usize, usize), usize> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `polish_contig_string` is never used [INFO] [stdout] --> src/graph/polish.rs:99:8 [INFO] [stdout] | [INFO] [stdout] 99 | pub fn polish_contig_string(contig: &str, aligned_reads: &[String], correction_threshold: f32) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `hybrid_polish_contig` is never used [INFO] [stdout] --> src/graph/polish.rs:157:8 [INFO] [stdout] | [INFO] [stdout] 157 | pub fn hybrid_polish_contig( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_and_parse_gfa_paths` is never used [INFO] [stdout] --> src/graph/navigation.rs:60:8 [INFO] [stdout] | [INFO] [stdout] 60 | pub fn load_and_parse_gfa_paths(path: &str) -> Result>, std::io::Error> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_oriented_sequence` is never used [INFO] [stdout] --> src/graph/navigation.rs:88:8 [INFO] [stdout] | [INFO] [stdout] 88 | pub fn get_oriented_sequence(segment: &str, dir: char, map: &HashMap) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `revcomp` is never used [INFO] [stdout] --> src/graph/navigation.rs:98:8 [INFO] [stdout] | [INFO] [stdout] 98 | pub fn revcomp(seq: &str) -> String { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `extract_path_metadata` is never used [INFO] [stdout] --> src/graph/navigation.rs:159:8 [INFO] [stdout] | [INFO] [stdout] 159 | pub fn extract_path_metadata( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `PathMetadata` is never constructed [INFO] [stdout] --> src/graph/navigation.rs:180:12 [INFO] [stdout] | [INFO] [stdout] 180 | pub struct PathMetadata { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `with_strand`, `with_tpm`, and `with_splicing` are never used [INFO] [stdout] --> src/graph/transcript.rs:53:12 [INFO] [stdout] | [INFO] [stdout] 36 | impl Transcript { [INFO] [stdout] | --------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 53 | pub fn with_strand(mut self, strand: char) -> Self { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 59 | pub fn with_tpm(mut self, tpm: f64) -> Self { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 65 | pub fn with_splicing(mut self, splicing: String) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `transcript_to_fasta` is never used [INFO] [stdout] --> src/graph/transcript.rs:199:8 [INFO] [stdout] | [INFO] [stdout] 199 | pub fn transcript_to_fasta(transcript: &Transcript) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `transcript_to_gfa_path` is never used [INFO] [stdout] --> src/graph/transcript.rs:211:8 [INFO] [stdout] | [INFO] [stdout] 211 | pub fn transcript_to_gfa_path(transcript: &Transcript) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `edit_distance` is never used [INFO] [stdout] --> src/graph/isoform_filter.rs:7:4 [INFO] [stdout] | [INFO] [stdout] 7 | fn edit_distance(a: &str, b: &str) -> usize { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_sequence_similarity` is never used [INFO] [stdout] --> src/graph/isoform_filter.rs:42:4 [INFO] [stdout] | [INFO] [stdout] 42 | fn calculate_sequence_similarity(t1: &Transcript, t2: &Transcript) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_path_similarity` is never used [INFO] [stdout] --> src/graph/isoform_filter.rs:54:4 [INFO] [stdout] | [INFO] [stdout] 54 | fn calculate_path_similarity(t1: &Transcript, t2: &Transcript) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_transcript_similarity` is never used [INFO] [stdout] --> src/graph/isoform_filter.rs:70:8 [INFO] [stdout] | [INFO] [stdout] 70 | pub fn calculate_transcript_similarity(t1: &Transcript, t2: &Transcript) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `cluster_similar_transcripts` is never used [INFO] [stdout] --> src/graph/isoform_filter.rs:79:8 [INFO] [stdout] | [INFO] [stdout] 79 | pub fn cluster_similar_transcripts( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `max_depth`, `bubble_count`, and `branchiness` are never read [INFO] [stdout] --> src/graph/complexity.rs:21:9 [INFO] [stdout] | [INFO] [stdout] 10 | pub struct PathStats { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 21 | pub max_depth: usize, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 24 | pub bubble_count: usize, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 27 | pub branchiness: f64, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `PathStats` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parallel_path_discovery` is never used [INFO] [stdout] --> src/graph/isoform_parallel.rs:9:8 [INFO] [stdout] | [INFO] [stdout] 9 | pub fn parallel_path_discovery( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parallel_transcript_assembly` is never used [INFO] [stdout] --> src/graph/isoform_parallel.rs:35:8 [INFO] [stdout] | [INFO] [stdout] 35 | pub fn parallel_transcript_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `assemble_single_transcript` is never used [INFO] [stdout] --> src/graph/isoform_parallel.rs:59:4 [INFO] [stdout] | [INFO] [stdout] 59 | fn assemble_single_transcript( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parallel_path_filtering` is never used [INFO] [stdout] --> src/graph/isoform_parallel.rs:95:8 [INFO] [stdout] | [INFO] [stdout] 95 | pub fn parallel_path_filtering( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_path_confidence` is never used [INFO] [stdout] --> src/graph/isoform_parallel.rs:106:4 [INFO] [stdout] | [INFO] [stdout] 106 | fn calculate_path_confidence(graph: &IsoformGraph, path: &[usize]) -> f32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `match_kmers_simd` is never used [INFO] [stdout] --> src/accel/simd.rs:64:8 [INFO] [stdout] | [INFO] [stdout] 64 | pub fn match_kmers_simd(a: &[u8], b: &[u8], max_mismatches: usize) -> bool { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `batch_match_kmers_simd` is never used [INFO] [stdout] --> src/accel/simd.rs:103:8 [INFO] [stdout] | [INFO] [stdout] 103 | pub fn batch_match_kmers_simd<'a>( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_best_overlap` is never used [INFO] [stdout] --> src/accel/simd.rs:121:4 [INFO] [stdout] | [INFO] [stdout] 121 | fn find_best_overlap(query: &[u8], target: &[u8], min_overlap: usize, max_distance: usize) -> (Option<(usize, usize)>, usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `GpuKmerCounter` is never constructed [INFO] [stdout] --> src/accel/gpu.rs:8:16 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct GpuKmerCounter { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new` and `count` are never used [INFO] [stdout] --> src/accel/gpu.rs:14:16 [INFO] [stdout] | [INFO] [stdout] 13 | impl GpuKmerCounter { [INFO] [stdout] | ------------------- associated items in this implementation [INFO] [stdout] 14 | pub fn new(_k: usize, expected_reads: usize) -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 21 | pub fn count(&self, sequences: &[String], k: usize) -> Vec { [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `partition_by_minimizer` is never used [INFO] [stdout] --> src/dist/partition.rs:8:8 [INFO] [stdout] | [INFO] [stdout] 8 | pub fn partition_by_minimizer(sequences: &[String], k: usize, buckets: usize) -> HashMap> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `save_partitions` is never used [INFO] [stdout] --> src/dist/partition.rs:31:8 [INFO] [stdout] | [INFO] [stdout] 31 | pub fn save_partitions(partitions: &HashMap>, output_dir: &str, prefix: &str) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `minimizer` is never used [INFO] [stdout] --> src/dist/partition.rs:56:4 [INFO] [stdout] | [INFO] [stdout] 56 | fn minimizer(kmer: &[u8], m: usize) -> u64 { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_minimizer_positions` is never used [INFO] [stdout] --> src/dist/partition.rs:68:8 [INFO] [stdout] | [INFO] [stdout] 68 | pub fn find_minimizer_positions(seq: &str, k: usize, m: usize) -> Vec<(usize, u64)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `DistributedConfig` is never constructed [INFO] [stdout] --> src/dist/scheduler.rs:7:12 [INFO] [stdout] | [INFO] [stdout] 7 | pub struct DistributedConfig { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `run_parallel_assembly` is never used [INFO] [stdout] --> src/dist/scheduler.rs:33:8 [INFO] [stdout] | [INFO] [stdout] 33 | pub fn run_parallel_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `generate_slurm_script` is never used [INFO] [stdout] --> src/dist/scheduler.rs:78:4 [INFO] [stdout] | [INFO] [stdout] 78 | fn generate_slurm_script( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `submit_slurm_jobs` is never used [INFO] [stdout] --> src/dist/scheduler.rs:107:8 [INFO] [stdout] | [INFO] [stdout] 107 | pub fn submit_slurm_jobs( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `run_distributed_assembly` is never used [INFO] [stdout] --> src/dist/scheduler.rs:163:8 [INFO] [stdout] | [INFO] [stdout] 163 | pub fn run_distributed_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `assemble_reads` is never used [INFO] [stdout] --> src/pipeline/assemble.rs:18:8 [INFO] [stdout] | [INFO] [stdout] 18 | pub fn assemble_reads( [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `distributed_assembly` is never used [INFO] [stdout] --> src/pipeline/assemble.rs:545:8 [INFO] [stdout] | [INFO] [stdout] 545 | pub fn distributed_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_contig_coverages` is never used [INFO] [stdout] --> src/pipeline/isoform_processor.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 14 | pub fn load_contig_coverages(expression_path: &str) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `is_gpu_available` is never used [INFO] [stdout] --> src/gpu/kmer_gpu.rs:86:8 [INFO] [stdout] | [INFO] [stdout] 86 | pub fn is_gpu_available() -> bool { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `normalize_kmers_gpu` is never used [INFO] [stdout] --> src/gpu/kmer_gpu.rs:113:8 [INFO] [stdout] | [INFO] [stdout] 113 | pub fn normalize_kmers_gpu(_kmers: &[String], _target_coverage: u32) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `count_kmers_gpu` is never used [INFO] [stdout] --> src/gpu/kmer_gpu.rs:138:8 [INFO] [stdout] | [INFO] [stdout] 138 | pub fn count_kmers_gpu(_sequences: &[String], _k: usize) -> HashMap { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `Stats` is never constructed [INFO] [stdout] --> src/cli/stats.rs:6:12 [INFO] [stdout] | [INFO] [stdout] 6 | pub struct Stats { [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_stats` is never used [INFO] [stdout] --> src/cli/stats.rs:13:8 [INFO] [stdout] | [INFO] [stdout] 13 | pub fn calculate_stats(path: &str) -> Stats { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `read_tpm_matrix` is never used [INFO] [stdout] --> src/quant/matrix.rs:32:8 [INFO] [stdout] | [INFO] [stdout] 32 | pub fn read_tpm_matrix(path: &str) -> std::io::Result>> { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `DiffExpResult` is never constructed [INFO] [stdout] --> src/quant/diffexp.rs:3:12 [INFO] [stdout] | [INFO] [stdout] 3 | pub struct DiffExpResult { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait `Log2` is never used [INFO] [stdout] --> src/quant/diffexp.rs:10:11 [INFO] [stdout] | [INFO] [stdout] 10 | pub trait Log2 { [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compute_fold_change_matrix` is never used [INFO] [stdout] --> src/quant/diffexp.rs:20:8 [INFO] [stdout] | [INFO] [stdout] 20 | pub fn compute_fold_change_matrix( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `t_test` is never used [INFO] [stdout] --> src/quant/diffexp.rs:47:4 [INFO] [stdout] | [INFO] [stdout] 47 | fn t_test(a: &[f64], b: &[f64]) -> f64 { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `variance` is never used [INFO] [stdout] --> src/quant/diffexp.rs:63:4 [INFO] [stdout] | [INFO] [stdout] 63 | fn variance(x: &[f64]) -> f64 { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `write_diffexp` is never used [INFO] [stdout] --> src/quant/diffexp.rs:69:8 [INFO] [stdout] | [INFO] [stdout] 69 | pub fn write_diffexp(results: &[DiffExpResult], output: &str) { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `estimate_tpm_from_bam` is never used [INFO] [stdout] --> src/quant/align_counts.rs:13:8 [INFO] [stdout] | [INFO] [stdout] 13 | pub fn estimate_tpm_from_bam(_bam_path: &str, transcripts: &[Transcript]) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `update_transcripts_with_tpm` is never used [INFO] [stdout] --> src/quant/align_counts.rs:63:8 [INFO] [stdout] | [INFO] [stdout] 63 | pub fn update_transcripts_with_tpm(transcripts: &mut [Transcript], bam_path: &str) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `filter_by_tpm` is never used [INFO] [stdout] --> src/quant/align_counts.rs:81:8 [INFO] [stdout] | [INFO] [stdout] 81 | pub fn filter_by_tpm(transcripts: Vec, min_tpm: f64) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `create_expression_matrix` is never used [INFO] [stdout] --> src/quant/align_counts.rs:95:8 [INFO] [stdout] | [INFO] [stdout] 95 | pub fn create_expression_matrix( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_counts_matrix` is never used [INFO] [stdout] --> src/quant/align_counts.rs:135:8 [INFO] [stdout] | [INFO] [stdout] 135 | pub fn load_counts_matrix(csv_path: &str, transcripts: &[Transcript]) -> Result>> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `tpm_to_counts` is never used [INFO] [stdout] --> src/quant/align_counts.rs:164:8 [INFO] [stdout] | [INFO] [stdout] 164 | pub fn tpm_to_counts(transcripts: &[Transcript], tpm_values: &[f64]) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `count_expressed_transcripts` is never used [INFO] [stdout] --> src/quant/align_counts.rs:194:8 [INFO] [stdout] | [INFO] [stdout] 194 | pub fn count_expressed_transcripts(transcripts: &[Transcript], tpm_values: &[f64], threshold: f64) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `estimate_transcript_abundances_from_alignments` is never used [INFO] [stdout] --> src/quant/align_counts.rs:212:8 [INFO] [stdout] | [INFO] [stdout] 212 | pub fn estimate_transcript_abundances_from_alignments(transcripts: &[Transcript], _bam_path: &str) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `polish_transcripts_with_long_reads` is never used [INFO] [stdout] --> src/polish/longread.rs:106:8 [INFO] [stdout] | [INFO] [stdout] 106 | pub fn polish_transcripts_with_long_reads( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_aligned_reads` is never used [INFO] [stdout] --> src/polish/longread.rs:135:4 [INFO] [stdout] | [INFO] [stdout] 135 | fn find_aligned_reads(transcript_seq: &str, long_reads: &[FastqRecord]) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `polish_sequence` is never used [INFO] [stdout] --> src/polish/longread.rs:163:4 [INFO] [stdout] | [INFO] [stdout] 163 | fn polish_sequence(seq: &str, reads: &[FastqRecord]) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_approximate_position` is never used [INFO] [stdout] --> src/polish/longread.rs:189:4 [INFO] [stdout] | [INFO] [stdout] 189 | fn find_approximate_position(reference: &str, read: &str) -> Option { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `update_consensus_counts` is never used [INFO] [stdout] --> src/polish/longread.rs:203:4 [INFO] [stdout] | [INFO] [stdout] 203 | fn update_consensus_counts(counts: &mut Vec<[u32; 5]>, start_pos: usize, read_seq: &str) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `build_consensus_sequence` is never used [INFO] [stdout] --> src/polish/longread.rs:229:4 [INFO] [stdout] | [INFO] [stdout] 229 | fn build_consensus_sequence(counts: &Vec<[u32; 5]>) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `TranscriptLocation` is never constructed [INFO] [stdout] --> src/eval/gtf_compare.rs:8:12 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct TranscriptLocation { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_gtf_ranges` is never used [INFO] [stdout] --> src/eval/gtf_compare.rs:16:8 [INFO] [stdout] | [INFO] [stdout] 16 | pub fn load_gtf_ranges(path: &str) -> IoResult> { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compare_gtf` is never used [INFO] [stdout] --> src/eval/gtf_compare.rs:74:8 [INFO] [stdout] | [INFO] [stdout] 74 | pub fn compare_gtf(truth: &str, predicted: &str) -> IoResult<(usize, usize, usize)> { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_metrics` is never used [INFO] [stdout] --> src/eval/gtf_compare.rs:87:8 [INFO] [stdout] | [INFO] [stdout] 87 | pub fn calculate_metrics(tp: usize, fp: usize, fn_: usize) -> (f64, f64, f64) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_exon_intervals` is never used [INFO] [stdout] --> src/eval/gtf_compare.rs:110:8 [INFO] [stdout] | [INFO] [stdout] 110 | pub fn load_exon_intervals( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compare_gtf_advanced` is never used [INFO] [stdout] --> src/eval/gtf_compare.rs:168:8 [INFO] [stdout] | [INFO] [stdout] 168 | pub fn compare_gtf_advanced( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compare_gfa` is never used [INFO] [stdout] --> src/eval/mod.rs:140:12 [INFO] [stdout] | [INFO] [stdout] 140 | pub fn compare_gfa(truth_path: &str, pred_path: &str) -> io::Result<(usize, usize, usize)> { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_gfa_paths` is never used [INFO] [stdout] --> src/eval/mod.rs:155:8 [INFO] [stdout] | [INFO] [stdout] 155 | fn load_gfa_paths(path: &str) -> io::Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `plot_pca_simple` is never used [INFO] [stdout] --> src/visualize/pca.rs:129:8 [INFO] [stdout] | [INFO] [stdout] 129 | pub fn plot_pca_simple(pca_result: &Array2, output: &str) -> Result<(), Box> { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `plot_heatmap` is never used [INFO] [stdout] --> src/visualize/plot.rs:5:8 [INFO] [stdout] | [INFO] [stdout] 5 | pub fn plot_heatmap(matrix: &Array2, output: &str) -> Result<(), Box> { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `threads` [INFO] [stdout] --> src/main.rs:38:13 [INFO] [stdout] | [INFO] [stdout] 38 | threads, [INFO] [stdout] | ^^^^^^^ help: try ignoring the field: `threads: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `coverage_target` [INFO] [stdout] --> src/main.rs:40:13 [INFO] [stdout] | [INFO] [stdout] 40 | coverage_target, [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: try ignoring the field: `coverage_target: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `max_reads` [INFO] [stdout] --> src/main.rs:41:13 [INFO] [stdout] | [INFO] [stdout] 41 | max_reads [INFO] [stdout] | ^^^^^^^^^ help: try ignoring the field: `max_reads: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `threads` [INFO] [stdout] --> src/main.rs:62:13 [INFO] [stdout] | [INFO] [stdout] 62 | threads, [INFO] [stdout] | ^^^^^^^ help: try ignoring the field: `threads: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `distributed` [INFO] [stdout] --> src/main.rs:66:13 [INFO] [stdout] | [INFO] [stdout] 66 | distributed, [INFO] [stdout] | ^^^^^^^^^^^ help: try ignoring the field: `distributed: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `buckets` [INFO] [stdout] --> src/main.rs:67:13 [INFO] [stdout] | [INFO] [stdout] 67 | buckets, [INFO] [stdout] | ^^^^^^^ help: try ignoring the field: `buckets: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `min_path_len` [INFO] [stdout] --> src/main.rs:83:13 [INFO] [stdout] | [INFO] [stdout] 83 | min_path_len, [INFO] [stdout] | ^^^^^^^^^^^^ help: try ignoring the field: `min_path_len: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `dev_mode` [INFO] [stdout] --> src/main.rs:84:13 [INFO] [stdout] | [INFO] [stdout] 84 | dev_mode, [INFO] [stdout] | ^^^^^^^^ help: try ignoring the field: `dev_mode: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `output` [INFO] [stdout] --> src/main.rs:437:39 [INFO] [stdout] | [INFO] [stdout] 437 | Commands::Visualize { matrix, output, heatmap, pca, components } => { [INFO] [stdout] | ^^^^^^ help: try ignoring the field: `output: _` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `read_long_reads` is never used [INFO] [stdout] --> src/io/fastq.rs:180:8 [INFO] [stdout] | [INFO] [stdout] 180 | pub fn read_long_reads(path: &str) -> io::Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `write_record` is never used [INFO] [stdout] --> src/io/fasta.rs:37:12 [INFO] [stdout] | [INFO] [stdout] 26 | impl FastaWriter { [INFO] [stdout] | ---------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 37 | pub fn write_record(&mut self, header: &str, sequence: &str) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `write_paths` is never used [INFO] [stdout] --> src/io/gfa.rs:40:12 [INFO] [stdout] | [INFO] [stdout] 12 | impl GfaWriter { [INFO] [stdout] | -------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 40 | pub fn write_paths(&mut self, contigs: &[Contig]) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `with_coverage` is never used [INFO] [stdout] --> src/io/gfa2.rs:25:12 [INFO] [stdout] | [INFO] [stdout] 14 | impl Gfa2Writer { [INFO] [stdout] | --------------- associated function in this implementation [INFO] [stdout] ... [INFO] [stdout] 25 | pub fn with_coverage(path: &str, coverage: HashMap) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `write_detailed_gff3` is never used [INFO] [stdout] --> src/io/gff3.rs:45:8 [INFO] [stdout] | [INFO] [stdout] 45 | pub fn write_detailed_gff3( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `write_detailed_gtf` is never used [INFO] [stdout] --> src/io/gtf.rs:70:8 [INFO] [stdout] | [INFO] [stdout] 70 | pub fn write_detailed_gtf( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `integrate_long_reads_for_polishing` is never used [INFO] [stdout] --> src/io/longread.rs:55:8 [INFO] [stdout] | [INFO] [stdout] 55 | pub fn integrate_long_reads_for_polishing( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `export_path_metadata_json` is never used [INFO] [stdout] --> src/io/odgi.rs:128:8 [INFO] [stdout] | [INFO] [stdout] 128 | pub fn export_path_metadata_json( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `export_odgi_paths` is never used [INFO] [stdout] --> src/io/export.rs:61:8 [INFO] [stdout] | [INFO] [stdout] 61 | pub fn export_odgi_paths( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `export_dot_graph` is never used [INFO] [stdout] --> src/io/export.rs:82:8 [INFO] [stdout] | [INFO] [stdout] 82 | pub fn export_dot_graph( [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `create_test_contigs` is never used [INFO] [stdout] --> src/io/metadata.rs:112:8 [INFO] [stdout] | [INFO] [stdout] 112 | fn create_test_contigs() -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type alias `Kmer` is never used [INFO] [stdout] --> src/kmer/kmer.rs:1:10 [INFO] [stdout] | [INFO] [stdout] 1 | pub type Kmer = String; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `encode_kmer` is never used [INFO] [stdout] --> src/kmer/kmer.rs:4:8 [INFO] [stdout] | [INFO] [stdout] 4 | pub fn encode_kmer(seq: &str) -> Option { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `AbundanceStats` is never constructed [INFO] [stdout] --> src/kmer/normalize.rs:8:12 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct AbundanceStats { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `estimate_read_abundance` is never used [INFO] [stdout] --> src/kmer/normalize.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 14 | pub fn estimate_read_abundance(seq: &str, k: usize, sketch: &[u32]) -> AbundanceStats { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `median` is never used [INFO] [stdout] --> src/kmer/normalize.rs:105:4 [INFO] [stdout] | [INFO] [stdout] 105 | fn median(values: &mut [u16]) -> u16 { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_repeat_positions` is never used [INFO] [stdout] --> src/kmer/repeat.rs:28:8 [INFO] [stdout] | [INFO] [stdout] 28 | pub fn find_repeat_positions(seq: &str, pattern: &str, min_len: usize) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `kmer_path` is never read [INFO] [stdout] --> src/graph/assembler.rs:10:9 [INFO] [stdout] | [INFO] [stdout] 7 | pub struct Contig { [INFO] [stdout] | ------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 10 | pub kmer_path: Vec, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Contig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `to_rle` is never used [INFO] [stdout] --> src/graph/assembler.rs:15:12 [INFO] [stdout] | [INFO] [stdout] 13 | impl Contig { [INFO] [stdout] | ----------- method in this implementation [INFO] [stdout] 14 | /// Convert the contig sequence to run-length encoding [INFO] [stdout] 15 | pub fn to_rle(&self) -> Vec<(u8, u8)> { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `shift` is never read [INFO] [stdout] --> src/graph/stitch.rs:154:9 [INFO] [stdout] | [INFO] [stdout] 151 | pub struct OverlapInfo { [INFO] [stdout] | ----------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 154 | pub shift: usize, [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `OverlapInfo` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_paths_from_gfa` is never used [INFO] [stdout] --> src/graph/stitch.rs:158:8 [INFO] [stdout] | [INFO] [stdout] 158 | pub fn load_paths_from_gfa(gfa_path: &str) -> Result, std::io::Error> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `cluster_contigs` is never used [INFO] [stdout] --> src/graph/partition.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 14 | pub fn cluster_contigs(graph: &DiGraphMap) -> HashMap> { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `merge_small_clusters` is never used [INFO] [stdout] --> src/graph/partition.rs:46:8 [INFO] [stdout] | [INFO] [stdout] 46 | pub fn merge_small_clusters( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_cluster_similarity` is never used [INFO] [stdout] --> src/graph/partition.rs:96:4 [INFO] [stdout] | [INFO] [stdout] 96 | fn calculate_cluster_similarity( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `merge_clusters` is never used [INFO] [stdout] --> src/graph/partition.rs:117:8 [INFO] [stdout] | [INFO] [stdout] 117 | pub fn merge_clusters(clusters: Vec>, _distance_matrix: &[Vec], _contigs: &[String]) -> Vec> { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `get_all_pair_links` is never used [INFO] [stdout] --> src/graph/edge_weight.rs:55:12 [INFO] [stdout] | [INFO] [stdout] 36 | impl PairLinkTracker { [INFO] [stdout] | -------------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 55 | pub fn get_all_pair_links(&self) -> &HashMap<(usize, usize), usize> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `polish_contig_string` is never used [INFO] [stdout] --> src/graph/polish.rs:99:8 [INFO] [stdout] | [INFO] [stdout] 99 | pub fn polish_contig_string(contig: &str, aligned_reads: &[String], correction_threshold: f32) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `hybrid_polish_contig` is never used [INFO] [stdout] --> src/graph/polish.rs:157:8 [INFO] [stdout] | [INFO] [stdout] 157 | pub fn hybrid_polish_contig( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_and_parse_gfa_paths` is never used [INFO] [stdout] --> src/graph/navigation.rs:60:8 [INFO] [stdout] | [INFO] [stdout] 60 | pub fn load_and_parse_gfa_paths(path: &str) -> Result>, std::io::Error> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_oriented_sequence` is never used [INFO] [stdout] --> src/graph/navigation.rs:88:8 [INFO] [stdout] | [INFO] [stdout] 88 | pub fn get_oriented_sequence(segment: &str, dir: char, map: &HashMap) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `extract_path_metadata` is never used [INFO] [stdout] --> src/graph/navigation.rs:159:8 [INFO] [stdout] | [INFO] [stdout] 159 | pub fn extract_path_metadata( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `with_strand`, `with_tpm`, and `with_splicing` are never used [INFO] [stdout] --> src/graph/transcript.rs:53:12 [INFO] [stdout] | [INFO] [stdout] 36 | impl Transcript { [INFO] [stdout] | --------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 53 | pub fn with_strand(mut self, strand: char) -> Self { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 59 | pub fn with_tpm(mut self, tpm: f64) -> Self { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 65 | pub fn with_splicing(mut self, splicing: String) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `transcript_to_fasta` is never used [INFO] [stdout] --> src/graph/transcript.rs:199:8 [INFO] [stdout] | [INFO] [stdout] 199 | pub fn transcript_to_fasta(transcript: &Transcript) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `transcript_to_gfa_path` is never used [INFO] [stdout] --> src/graph/transcript.rs:211:8 [INFO] [stdout] | [INFO] [stdout] 211 | pub fn transcript_to_gfa_path(transcript: &Transcript) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_transcript_similarity` is never used [INFO] [stdout] --> src/graph/isoform_filter.rs:70:8 [INFO] [stdout] | [INFO] [stdout] 70 | pub fn calculate_transcript_similarity(t1: &Transcript, t2: &Transcript) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `cluster_similar_transcripts` is never used [INFO] [stdout] --> src/graph/isoform_filter.rs:79:8 [INFO] [stdout] | [INFO] [stdout] 79 | pub fn cluster_similar_transcripts( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `max_depth`, `bubble_count`, and `branchiness` are never read [INFO] [stdout] --> src/graph/complexity.rs:21:9 [INFO] [stdout] | [INFO] [stdout] 10 | pub struct PathStats { [INFO] [stdout] | --------- fields in this struct [INFO] [stdout] ... [INFO] [stdout] 21 | pub max_depth: usize, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 24 | pub bubble_count: usize, [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 27 | pub branchiness: f64, [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `PathStats` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parallel_path_discovery` is never used [INFO] [stdout] --> src/graph/isoform_parallel.rs:9:8 [INFO] [stdout] | [INFO] [stdout] 9 | pub fn parallel_path_discovery( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `parallel_path_filtering` is never used [INFO] [stdout] --> src/graph/isoform_parallel.rs:95:8 [INFO] [stdout] | [INFO] [stdout] 95 | pub fn parallel_path_filtering( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_path_confidence` is never used [INFO] [stdout] --> src/graph/isoform_parallel.rs:106:4 [INFO] [stdout] | [INFO] [stdout] 106 | fn calculate_path_confidence(graph: &IsoformGraph, path: &[usize]) -> f32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `batch_match_kmers_simd` is never used [INFO] [stdout] --> src/accel/simd.rs:103:8 [INFO] [stdout] | [INFO] [stdout] 103 | pub fn batch_match_kmers_simd<'a>( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_best_overlap` is never used [INFO] [stdout] --> src/accel/simd.rs:121:4 [INFO] [stdout] | [INFO] [stdout] 121 | fn find_best_overlap(query: &[u8], target: &[u8], min_overlap: usize, max_distance: usize) -> (Option<(usize, usize)>, usize) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `GpuKmerCounter` is never constructed [INFO] [stdout] --> src/accel/gpu.rs:8:16 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct GpuKmerCounter { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `new` and `count` are never used [INFO] [stdout] --> src/accel/gpu.rs:14:16 [INFO] [stdout] | [INFO] [stdout] 13 | impl GpuKmerCounter { [INFO] [stdout] | ------------------- associated items in this implementation [INFO] [stdout] 14 | pub fn new(_k: usize, expected_reads: usize) -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] ... [INFO] [stdout] 21 | pub fn count(&self, sequences: &[String], k: usize) -> Vec { [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `save_partitions` is never used [INFO] [stdout] --> src/dist/partition.rs:31:8 [INFO] [stdout] | [INFO] [stdout] 31 | pub fn save_partitions(partitions: &HashMap>, output_dir: &str, prefix: &str) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `minimizer` is never used [INFO] [stdout] --> src/dist/partition.rs:56:4 [INFO] [stdout] | [INFO] [stdout] 56 | fn minimizer(kmer: &[u8], m: usize) -> u64 { [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_minimizer_positions` is never used [INFO] [stdout] --> src/dist/partition.rs:68:8 [INFO] [stdout] | [INFO] [stdout] 68 | pub fn find_minimizer_positions(seq: &str, k: usize, m: usize) -> Vec<(usize, u64)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `DistributedConfig` is never constructed [INFO] [stdout] --> src/dist/scheduler.rs:7:12 [INFO] [stdout] | [INFO] [stdout] 7 | pub struct DistributedConfig { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `run_parallel_assembly` is never used [INFO] [stdout] --> src/dist/scheduler.rs:33:8 [INFO] [stdout] | [INFO] [stdout] 33 | pub fn run_parallel_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `generate_slurm_script` is never used [INFO] [stdout] --> src/dist/scheduler.rs:78:4 [INFO] [stdout] | [INFO] [stdout] 78 | fn generate_slurm_script( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `submit_slurm_jobs` is never used [INFO] [stdout] --> src/dist/scheduler.rs:107:8 [INFO] [stdout] | [INFO] [stdout] 107 | pub fn submit_slurm_jobs( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `run_distributed_assembly` is never used [INFO] [stdout] --> src/dist/scheduler.rs:163:8 [INFO] [stdout] | [INFO] [stdout] 163 | pub fn run_distributed_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `assemble_reads` is never used [INFO] [stdout] --> src/pipeline/assemble.rs:18:8 [INFO] [stdout] | [INFO] [stdout] 18 | pub fn assemble_reads( [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `distributed_assembly` is never used [INFO] [stdout] --> src/pipeline/assemble.rs:545:8 [INFO] [stdout] | [INFO] [stdout] 545 | pub fn distributed_assembly( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_contig_coverages` is never used [INFO] [stdout] --> src/pipeline/isoform_processor.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 14 | pub fn load_contig_coverages(expression_path: &str) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `is_gpu_available` is never used [INFO] [stdout] --> src/gpu/kmer_gpu.rs:86:8 [INFO] [stdout] | [INFO] [stdout] 86 | pub fn is_gpu_available() -> bool { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `normalize_kmers_gpu` is never used [INFO] [stdout] --> src/gpu/kmer_gpu.rs:113:8 [INFO] [stdout] | [INFO] [stdout] 113 | pub fn normalize_kmers_gpu(_kmers: &[String], _target_coverage: u32) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `count_kmers_gpu` is never used [INFO] [stdout] --> src/gpu/kmer_gpu.rs:138:8 [INFO] [stdout] | [INFO] [stdout] 138 | pub fn count_kmers_gpu(_sequences: &[String], _k: usize) -> HashMap { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `read_tpm_matrix` is never used [INFO] [stdout] --> src/quant/matrix.rs:32:8 [INFO] [stdout] | [INFO] [stdout] 32 | pub fn read_tpm_matrix(path: &str) -> std::io::Result>> { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `DiffExpResult` is never constructed [INFO] [stdout] --> src/quant/diffexp.rs:3:12 [INFO] [stdout] | [INFO] [stdout] 3 | pub struct DiffExpResult { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait `Log2` is never used [INFO] [stdout] --> src/quant/diffexp.rs:10:11 [INFO] [stdout] | [INFO] [stdout] 10 | pub trait Log2 { [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compute_fold_change_matrix` is never used [INFO] [stdout] --> src/quant/diffexp.rs:20:8 [INFO] [stdout] | [INFO] [stdout] 20 | pub fn compute_fold_change_matrix( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `t_test` is never used [INFO] [stdout] --> src/quant/diffexp.rs:47:4 [INFO] [stdout] | [INFO] [stdout] 47 | fn t_test(a: &[f64], b: &[f64]) -> f64 { [INFO] [stdout] | ^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `variance` is never used [INFO] [stdout] --> src/quant/diffexp.rs:63:4 [INFO] [stdout] | [INFO] [stdout] 63 | fn variance(x: &[f64]) -> f64 { [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `write_diffexp` is never used [INFO] [stdout] --> src/quant/diffexp.rs:69:8 [INFO] [stdout] | [INFO] [stdout] 69 | pub fn write_diffexp(results: &[DiffExpResult], output: &str) { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `estimate_tpm_from_bam` is never used [INFO] [stdout] --> src/quant/align_counts.rs:13:8 [INFO] [stdout] | [INFO] [stdout] 13 | pub fn estimate_tpm_from_bam(_bam_path: &str, transcripts: &[Transcript]) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `update_transcripts_with_tpm` is never used [INFO] [stdout] --> src/quant/align_counts.rs:63:8 [INFO] [stdout] | [INFO] [stdout] 63 | pub fn update_transcripts_with_tpm(transcripts: &mut [Transcript], bam_path: &str) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `filter_by_tpm` is never used [INFO] [stdout] --> src/quant/align_counts.rs:81:8 [INFO] [stdout] | [INFO] [stdout] 81 | pub fn filter_by_tpm(transcripts: Vec, min_tpm: f64) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `create_expression_matrix` is never used [INFO] [stdout] --> src/quant/align_counts.rs:95:8 [INFO] [stdout] | [INFO] [stdout] 95 | pub fn create_expression_matrix( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_counts_matrix` is never used [INFO] [stdout] --> src/quant/align_counts.rs:135:8 [INFO] [stdout] | [INFO] [stdout] 135 | pub fn load_counts_matrix(csv_path: &str, transcripts: &[Transcript]) -> Result>> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `tpm_to_counts` is never used [INFO] [stdout] --> src/quant/align_counts.rs:164:8 [INFO] [stdout] | [INFO] [stdout] 164 | pub fn tpm_to_counts(transcripts: &[Transcript], tpm_values: &[f64]) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `count_expressed_transcripts` is never used [INFO] [stdout] --> src/quant/align_counts.rs:194:8 [INFO] [stdout] | [INFO] [stdout] 194 | pub fn count_expressed_transcripts(transcripts: &[Transcript], tpm_values: &[f64], threshold: f64) -> Result { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `estimate_transcript_abundances_from_alignments` is never used [INFO] [stdout] --> src/quant/align_counts.rs:212:8 [INFO] [stdout] | [INFO] [stdout] 212 | pub fn estimate_transcript_abundances_from_alignments(transcripts: &[Transcript], _bam_path: &str) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `polish_transcripts_with_long_reads` is never used [INFO] [stdout] --> src/polish/longread.rs:106:8 [INFO] [stdout] | [INFO] [stdout] 106 | pub fn polish_transcripts_with_long_reads( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_aligned_reads` is never used [INFO] [stdout] --> src/polish/longread.rs:135:4 [INFO] [stdout] | [INFO] [stdout] 135 | fn find_aligned_reads(transcript_seq: &str, long_reads: &[FastqRecord]) -> Vec { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `polish_sequence` is never used [INFO] [stdout] --> src/polish/longread.rs:163:4 [INFO] [stdout] | [INFO] [stdout] 163 | fn polish_sequence(seq: &str, reads: &[FastqRecord]) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `find_approximate_position` is never used [INFO] [stdout] --> src/polish/longread.rs:189:4 [INFO] [stdout] | [INFO] [stdout] 189 | fn find_approximate_position(reference: &str, read: &str) -> Option { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `update_consensus_counts` is never used [INFO] [stdout] --> src/polish/longread.rs:203:4 [INFO] [stdout] | [INFO] [stdout] 203 | fn update_consensus_counts(counts: &mut Vec<[u32; 5]>, start_pos: usize, read_seq: &str) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `build_consensus_sequence` is never used [INFO] [stdout] --> src/polish/longread.rs:229:4 [INFO] [stdout] | [INFO] [stdout] 229 | fn build_consensus_sequence(counts: &Vec<[u32; 5]>) -> String { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `TranscriptLocation` is never constructed [INFO] [stdout] --> src/eval/gtf_compare.rs:8:12 [INFO] [stdout] | [INFO] [stdout] 8 | pub struct TranscriptLocation { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_gtf_ranges` is never used [INFO] [stdout] --> src/eval/gtf_compare.rs:16:8 [INFO] [stdout] | [INFO] [stdout] 16 | pub fn load_gtf_ranges(path: &str) -> IoResult> { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compare_gtf` is never used [INFO] [stdout] --> src/eval/gtf_compare.rs:74:8 [INFO] [stdout] | [INFO] [stdout] 74 | pub fn compare_gtf(truth: &str, predicted: &str) -> IoResult<(usize, usize, usize)> { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_metrics` is never used [INFO] [stdout] --> src/eval/gtf_compare.rs:87:8 [INFO] [stdout] | [INFO] [stdout] 87 | pub fn calculate_metrics(tp: usize, fp: usize, fn_: usize) -> (f64, f64, f64) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_exon_intervals` is never used [INFO] [stdout] --> src/eval/gtf_compare.rs:110:8 [INFO] [stdout] | [INFO] [stdout] 110 | pub fn load_exon_intervals( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compare_gtf_advanced` is never used [INFO] [stdout] --> src/eval/gtf_compare.rs:168:8 [INFO] [stdout] | [INFO] [stdout] 168 | pub fn compare_gtf_advanced( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `compare_gfa` is never used [INFO] [stdout] --> src/eval/mod.rs:140:12 [INFO] [stdout] | [INFO] [stdout] 140 | pub fn compare_gfa(truth_path: &str, pred_path: &str) -> io::Result<(usize, usize, usize)> { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_gfa_paths` is never used [INFO] [stdout] --> src/eval/mod.rs:155:8 [INFO] [stdout] | [INFO] [stdout] 155 | fn load_gfa_paths(path: &str) -> io::Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `plot_pca_simple` is never used [INFO] [stdout] --> src/visualize/pca.rs:129:8 [INFO] [stdout] | [INFO] [stdout] 129 | pub fn plot_pca_simple(pca_result: &Array2, output: &str) -> Result<(), Box> { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `plot_heatmap` is never used [INFO] [stdout] --> src/visualize/plot.rs:5:8 [INFO] [stdout] | [INFO] [stdout] 5 | pub fn plot_heatmap(matrix: &Array2, output: &str) -> Result<(), Box> { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 15s [INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1 [INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1` [INFO] running `Command { std: "docker" "inspect" "66fc035fe69e2123649556b7168890ba4d9ba24a61ad8b8fbab316ae97cc08e7", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "66fc035fe69e2123649556b7168890ba4d9ba24a61ad8b8fbab316ae97cc08e7", kill_on_drop: false }` [INFO] [stdout] 66fc035fe69e2123649556b7168890ba4d9ba24a61ad8b8fbab316ae97cc08e7