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[INFO] [stdout] warning: fields `genome_fasta` and `temp_files` are never read
[INFO] [stdout]   --> src/ins/finder.rs:40:5
[INFO] [stdout]    |
[INFO] [stdout] 38 | pub struct INSFinder {
[INFO] [stdout]    |            --------- fields in this struct
[INFO] [stdout] 39 |     bam_path: String,
[INFO] [stdout] 40 |     genome_fasta: String,
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] 41 |     config: INSFinderConfig,
[INFO] [stdout] 42 |     temp_files: HashSet<String>,
[INFO] [stdout]    |     ^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `bam_path` and `genome_fasta` are never read
[INFO] [stdout]    --> src/tre/mod.rs:159:5
[INFO] [stdout]     |
[INFO] [stdout] 157 | pub struct TREFinder {
[INFO] [stdout]     |            --------- fields in this struct
[INFO] [stdout] 158 |     /// BAM file path
[INFO] [stdout] 159 |     bam_path: String,
[INFO] [stdout]     |     ^^^^^^^^
[INFO] [stdout] 160 |     /// Reference genome FASTA path
[INFO] [stdout] 161 |     genome_fasta: String,
[INFO] [stdout]     |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `genome_fasta` and `temp_files` are never read
[INFO] [stdout]   --> src/ins/finder.rs:40:5
[INFO] [stdout]    |
[INFO] [stdout] 38 | pub struct INSFinder {
[INFO] [stdout]    |            --------- fields in this struct
[INFO] [stdout] 39 |     bam_path: String,
[INFO] [stdout] 40 |     genome_fasta: String,
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] 41 |     config: INSFinderConfig,
[INFO] [stdout] 42 |     temp_files: HashSet<String>,
[INFO] [stdout]    |     ^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `bam_path` and `genome_fasta` are never read
[INFO] [stdout]    --> src/tre/mod.rs:159:5
[INFO] [stdout]     |
[INFO] [stdout] 157 | pub struct TREFinder {
[INFO] [stdout]     |            --------- fields in this struct
[INFO] [stdout] 158 |     /// BAM file path
[INFO] [stdout] 159 |     bam_path: String,
[INFO] [stdout]     |     ^^^^^^^^
[INFO] [stdout] 160 |     /// Reference genome FASTA path
[INFO] [stdout] 161 |     genome_fasta: String,
[INFO] [stdout]     |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `etype` and `repeat_unit` are never read
[INFO] [stdout]   --> src/ins/mod.rs:26:9
[INFO] [stdout]    |
[INFO] [stdout] 12 | pub struct Insertion {
[INFO] [stdout]    |            --------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 26 |     pub etype: String,
[INFO] [stdout]    |         ^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 30 |     pub repeat_unit: Option<String>,
[INFO] [stdout]    |         ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `Insertion` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `extract_neighbor_seqs` and `to_bed` are never used
[INFO] [stdout]   --> src/ins/mod.rs:58:12
[INFO] [stdout]    |
[INFO] [stdout] 33 | impl Insertion {
[INFO] [stdout]    | -------------- associated items in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 58 |     pub fn extract_neighbor_seqs(read_seq: &str, rpos: usize, ins_size: usize, flank_size: usize) -> String {
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 83 |     pub fn to_bed(&self, include_read: bool) -> String {
[INFO] [stdout]    |            ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `flank_size`, `max_cov`, `nprocs`, `check_split_alignments`, `use_unpaired_clips`, and `debug` are never read
[INFO] [stdout]   --> src/ins/finder.rs:13:9
[INFO] [stdout]    |
[INFO] [stdout] 11 | pub struct INSFinderConfig {
[INFO] [stdout]    |            --------------- fields in this struct
[INFO] [stdout] 12 |     pub min_size: u32,
[INFO] [stdout] 13 |     pub flank_size: u32,
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] 14 |     pub max_cov: u32,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 15 |     pub min_support: u32,
[INFO] [stdout] 16 |     pub nprocs: usize,
[INFO] [stdout]    |         ^^^^^^
[INFO] [stdout] 17 |     pub check_split_alignments: bool,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 18 |     pub use_unpaired_clips: bool,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 19 |     pub debug: bool,
[INFO] [stdout]    |         ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `INSFinderConfig` 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: fields `genome_fasta` and `temp_files` are never read
[INFO] [stdout]   --> src/ins/finder.rs:40:5
[INFO] [stdout]    |
[INFO] [stdout] 38 | pub struct INSFinder {
[INFO] [stdout]    |            --------- fields in this struct
[INFO] [stdout] 39 |     bam_path: String,
[INFO] [stdout] 40 |     genome_fasta: String,
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] 41 |     config: INSFinderConfig,
[INFO] [stdout] 42 |     temp_files: HashSet<String>,
[INFO] [stdout]    |     ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `flank_size`, `nprocs`, and `include_partials` are never read
[INFO] [stdout]   --> src/tre/mod.rs:28:9
[INFO] [stdout]    |
[INFO] [stdout] 20 | pub struct TREFinderConfig {
[INFO] [stdout]    |            --------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 28 |     pub flank_size: u32,
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 32 |     pub nprocs: usize,
[INFO] [stdout]    |         ^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 48 |     pub include_partials: bool,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `TREFinderConfig` 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: multiple fields are never read
[INFO] [stdout]    --> src/tre/mod.rs:96:9
[INFO] [stdout]     |
[INFO] [stdout]  92 | pub struct TrfResult {
[INFO] [stdout]     |            --------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout]  96 |     pub end: i32,
[INFO] [stdout]     |         ^^^
[INFO] [stdout] ...
[INFO] [stdout] 100 |     pub copy_number: f64,
[INFO] [stdout]     |         ^^^^^^^^^^^
[INFO] [stdout] 101 |     /// Consensus size
[INFO] [stdout] 102 |     pub consensus_size: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^
[INFO] [stdout] 103 |     /// Percent matches
[INFO] [stdout] 104 |     pub percent_matches: f64,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^
[INFO] [stdout] 105 |     /// Percent indels
[INFO] [stdout] 106 |     pub percent_indels: f64,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^
[INFO] [stdout] 107 |     /// Score
[INFO] [stdout] 108 |     pub score: i32,
[INFO] [stdout]     |         ^^^^^
[INFO] [stdout] 109 |     /// A count
[INFO] [stdout] 110 |     pub a_count: i32,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 111 |     /// C count
[INFO] [stdout] 112 |     pub c_count: i32,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 113 |     /// G count
[INFO] [stdout] 114 |     pub g_count: i32,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 115 |     /// T count
[INFO] [stdout] 116 |     pub t_count: i32,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 117 |     /// Entropy
[INFO] [stdout] 118 |     pub entropy: f64,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `TrfResult` 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: multiple fields are never read
[INFO] [stdout]    --> src/tre/mod.rs:129:9
[INFO] [stdout]     |
[INFO] [stdout] 125 | pub struct BlastnResult {
[INFO] [stdout]     |            ------------ fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 129 |     pub subject_id: String,
[INFO] [stdout]     |         ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 133 |     pub alignment_length: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^
[INFO] [stdout] 134 |     /// Mismatches
[INFO] [stdout] 135 |     pub mismatches: i32,
[INFO] [stdout]     |         ^^^^^^^^^^
[INFO] [stdout] 136 |     /// Gap openings
[INFO] [stdout] 137 |     pub gap_openings: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^^
[INFO] [stdout] 138 |     /// Query start (1-based)
[INFO] [stdout] 139 |     pub query_start: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^
[INFO] [stdout] 140 |     /// Query end (1-based)
[INFO] [stdout] 141 |     pub query_end: i32,
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout] 142 |     /// Subject start (1-based)
[INFO] [stdout] 143 |     pub subject_start: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^^^
[INFO] [stdout] 144 |     /// Subject end (1-based)
[INFO] [stdout] 145 |     pub subject_end: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 149 |     pub bit_score: f64,
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout] 150 |     /// Query sequence
[INFO] [stdout] 151 |     pub query_seq: Option<String>,
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout] 152 |     /// Subject sequence
[INFO] [stdout] 153 |     pub subject_seq: Option<String>,
[INFO] [stdout]     |         ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `BlastnResult` 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: fields `bam_path` and `genome_fasta` are never read
[INFO] [stdout]    --> src/tre/mod.rs:159:5
[INFO] [stdout]     |
[INFO] [stdout] 157 | pub struct TREFinder {
[INFO] [stdout]     |            --------- fields in this struct
[INFO] [stdout] 158 |     /// BAM file path
[INFO] [stdout] 159 |     bam_path: String,
[INFO] [stdout]     |     ^^^^^^^^
[INFO] [stdout] 160 |     /// Reference genome FASTA path
[INFO] [stdout] 161 |     genome_fasta: String,
[INFO] [stdout]     |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `max_bad_cluster_size` is never read
[INFO] [stdout]   --> src/cluster/mod.rs:21:9
[INFO] [stdout]    |
[INFO] [stdout] 11 | pub struct ClusterParams {
[INFO] [stdout]    |            ------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 21 |     pub max_bad_cluster_size: usize,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `ClusterParams` 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: fields `genome_start`, `genome_end`, `repeat_seq`, and `fail_reason` are never read
[INFO] [stdout]   --> src/variant/mod.rs:22:9
[INFO] [stdout]    |
[INFO] [stdout] 10 | pub struct Allele {
[INFO] [stdout]    |            ------ fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 22 |     pub genome_start: i32,
[INFO] [stdout]    |         ^^^^^^^^^^^^
[INFO] [stdout] 23 |     /// Genome end position
[INFO] [stdout] 24 |     pub genome_end: i32,
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 28 |     pub repeat_seq: String,
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 36 |     pub fail_reason: Option<String>,
[INFO] [stdout]    |         ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `Allele` 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: fields `ref_motif`, `ref_seq`, and `ref_cn` are never read
[INFO] [stdout]    --> src/variant/mod.rs:114:9
[INFO] [stdout]     |
[INFO] [stdout]  96 | pub struct Variant {
[INFO] [stdout]     |            ------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 114 |     pub ref_motif: String,
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout] 115 |     /// Reference sequence
[INFO] [stdout] 116 |     pub ref_seq: String,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 117 |     /// Reference copy number
[INFO] [stdout] 118 |     pub ref_cn: f64,
[INFO] [stdout]     |         ^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `Variant` 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 `split_tasks` is never used
[INFO] [stdout]  --> src/utils/mod.rs:9:8
[INFO] [stdout]   |
[INFO] [stdout] 9 | pub fn split_tasks<T: Clone>(items: &[T], n: usize) -> Vec<Vec<T>> {
[INFO] [stdout]   |        ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `reverse_complement` is never used
[INFO] [stdout]   --> src/utils/mod.rs:34:8
[INFO] [stdout]    |
[INFO] [stdout] 34 | pub fn reverse_complement(seq: &str) -> String {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `merge_spans` is never used
[INFO] [stdout]   --> src/utils/mod.rs:49:8
[INFO] [stdout]    |
[INFO] [stdout] 49 | pub fn merge_spans(spans: &[(i32, i32)]) -> Vec<(i32, i32)> {
[INFO] [stdout]    |        ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `complement_spans` is never used
[INFO] [stdout]   --> src/utils/mod.rs:72:8
[INFO] [stdout]    |
[INFO] [stdout] 72 | pub fn complement_spans(spans: &[(i32, i32)], _min: i32, _max: i32) -> Vec<(i32, i32)> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_temp_file` is never used
[INFO] [stdout]    --> src/utils/mod.rs:111:8
[INFO] [stdout]     |
[INFO] [stdout] 111 | pub fn create_temp_file(content: &str, _suffix: &str) -> std::io::Result<NamedTempFile> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_bed_line` is never used
[INFO] [stdout]    --> src/utils/mod.rs:118:8
[INFO] [stdout]     |
[INFO] [stdout] 118 | pub fn parse_bed_line(line: &str) -> Option<(String, i32, i32, Option<String>)> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `read_bed_file` is never used
[INFO] [stdout]    --> src/utils/mod.rs:133:8
[INFO] [stdout]     |
[INFO] [stdout] 133 | pub fn read_bed_file<P: AsRef<Path>>(path: P) -> std::io::Result<Vec<(String, i32, i32, Option<String>)>> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `etype` and `repeat_unit` are never read
[INFO] [stdout]   --> src/ins/mod.rs:26:9
[INFO] [stdout]    |
[INFO] [stdout] 12 | pub struct Insertion {
[INFO] [stdout]    |            --------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 26 |     pub etype: String,
[INFO] [stdout]    |         ^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 30 |     pub repeat_unit: Option<String>,
[INFO] [stdout]    |         ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `Insertion` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `to_bed` is never used
[INFO] [stdout]   --> src/ins/mod.rs:83:12
[INFO] [stdout]    |
[INFO] [stdout] 33 | impl Insertion {
[INFO] [stdout]    | -------------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 83 |     pub fn to_bed(&self, include_read: bool) -> String {
[INFO] [stdout]    |            ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `flank_size`, `max_cov`, `nprocs`, `check_split_alignments`, `use_unpaired_clips`, and `debug` are never read
[INFO] [stdout]   --> src/ins/finder.rs:13:9
[INFO] [stdout]    |
[INFO] [stdout] 11 | pub struct INSFinderConfig {
[INFO] [stdout]    |            --------------- fields in this struct
[INFO] [stdout] 12 |     pub min_size: u32,
[INFO] [stdout] 13 |     pub flank_size: u32,
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] 14 |     pub max_cov: u32,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 15 |     pub min_support: u32,
[INFO] [stdout] 16 |     pub nprocs: usize,
[INFO] [stdout]    |         ^^^^^^
[INFO] [stdout] 17 |     pub check_split_alignments: bool,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 18 |     pub use_unpaired_clips: bool,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 19 |     pub debug: bool,
[INFO] [stdout]    |         ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `INSFinderConfig` 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: fields `genome_fasta` and `temp_files` are never read
[INFO] [stdout]   --> src/ins/finder.rs:40:5
[INFO] [stdout]    |
[INFO] [stdout] 38 | pub struct INSFinder {
[INFO] [stdout]    |            --------- fields in this struct
[INFO] [stdout] 39 |     bam_path: String,
[INFO] [stdout] 40 |     genome_fasta: String,
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] 41 |     config: INSFinderConfig,
[INFO] [stdout] 42 |     temp_files: HashSet<String>,
[INFO] [stdout]    |     ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `flank_size`, `nprocs`, and `include_partials` are never read
[INFO] [stdout]   --> src/tre/mod.rs:28:9
[INFO] [stdout]    |
[INFO] [stdout] 20 | pub struct TREFinderConfig {
[INFO] [stdout]    |            --------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 28 |     pub flank_size: u32,
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 32 |     pub nprocs: usize,
[INFO] [stdout]    |         ^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 48 |     pub include_partials: bool,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `TREFinderConfig` 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: multiple fields are never read
[INFO] [stdout]    --> src/tre/mod.rs:96:9
[INFO] [stdout]     |
[INFO] [stdout]  92 | pub struct TrfResult {
[INFO] [stdout]     |            --------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout]  96 |     pub end: i32,
[INFO] [stdout]     |         ^^^
[INFO] [stdout] ...
[INFO] [stdout] 100 |     pub copy_number: f64,
[INFO] [stdout]     |         ^^^^^^^^^^^
[INFO] [stdout] 101 |     /// Consensus size
[INFO] [stdout] 102 |     pub consensus_size: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^
[INFO] [stdout] 103 |     /// Percent matches
[INFO] [stdout] 104 |     pub percent_matches: f64,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^
[INFO] [stdout] 105 |     /// Percent indels
[INFO] [stdout] 106 |     pub percent_indels: f64,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^
[INFO] [stdout] 107 |     /// Score
[INFO] [stdout] 108 |     pub score: i32,
[INFO] [stdout]     |         ^^^^^
[INFO] [stdout] 109 |     /// A count
[INFO] [stdout] 110 |     pub a_count: i32,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 111 |     /// C count
[INFO] [stdout] 112 |     pub c_count: i32,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 113 |     /// G count
[INFO] [stdout] 114 |     pub g_count: i32,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 115 |     /// T count
[INFO] [stdout] 116 |     pub t_count: i32,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 117 |     /// Entropy
[INFO] [stdout] 118 |     pub entropy: f64,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `TrfResult` 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: multiple fields are never read
[INFO] [stdout]    --> src/tre/mod.rs:129:9
[INFO] [stdout]     |
[INFO] [stdout] 125 | pub struct BlastnResult {
[INFO] [stdout]     |            ------------ fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 129 |     pub subject_id: String,
[INFO] [stdout]     |         ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 133 |     pub alignment_length: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^
[INFO] [stdout] 134 |     /// Mismatches
[INFO] [stdout] 135 |     pub mismatches: i32,
[INFO] [stdout]     |         ^^^^^^^^^^
[INFO] [stdout] 136 |     /// Gap openings
[INFO] [stdout] 137 |     pub gap_openings: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^^
[INFO] [stdout] 138 |     /// Query start (1-based)
[INFO] [stdout] 139 |     pub query_start: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^
[INFO] [stdout] 140 |     /// Query end (1-based)
[INFO] [stdout] 141 |     pub query_end: i32,
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout] 142 |     /// Subject start (1-based)
[INFO] [stdout] 143 |     pub subject_start: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^^^
[INFO] [stdout] 144 |     /// Subject end (1-based)
[INFO] [stdout] 145 |     pub subject_end: i32,
[INFO] [stdout]     |         ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 149 |     pub bit_score: f64,
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout] 150 |     /// Query sequence
[INFO] [stdout] 151 |     pub query_seq: Option<String>,
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout] 152 |     /// Subject sequence
[INFO] [stdout] 153 |     pub subject_seq: Option<String>,
[INFO] [stdout]     |         ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `BlastnResult` 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: fields `bam_path` and `genome_fasta` are never read
[INFO] [stdout]    --> src/tre/mod.rs:159:5
[INFO] [stdout]     |
[INFO] [stdout] 157 | pub struct TREFinder {
[INFO] [stdout]     |            --------- fields in this struct
[INFO] [stdout] 158 |     /// BAM file path
[INFO] [stdout] 159 |     bam_path: String,
[INFO] [stdout]     |     ^^^^^^^^
[INFO] [stdout] 160 |     /// Reference genome FASTA path
[INFO] [stdout] 161 |     genome_fasta: String,
[INFO] [stdout]     |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `max_bad_cluster_size` is never read
[INFO] [stdout]   --> src/cluster/mod.rs:21:9
[INFO] [stdout]    |
[INFO] [stdout] 11 | pub struct ClusterParams {
[INFO] [stdout]    |            ------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 21 |     pub max_bad_cluster_size: usize,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `ClusterParams` 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: fields `genome_start`, `genome_end`, `repeat_seq`, and `fail_reason` are never read
[INFO] [stdout]   --> src/variant/mod.rs:22:9
[INFO] [stdout]    |
[INFO] [stdout] 10 | pub struct Allele {
[INFO] [stdout]    |            ------ fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 22 |     pub genome_start: i32,
[INFO] [stdout]    |         ^^^^^^^^^^^^
[INFO] [stdout] 23 |     /// Genome end position
[INFO] [stdout] 24 |     pub genome_end: i32,
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 28 |     pub repeat_seq: String,
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 36 |     pub fail_reason: Option<String>,
[INFO] [stdout]    |         ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `Allele` 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: fields `ref_motif` and `ref_seq` are never read
[INFO] [stdout]    --> src/variant/mod.rs:114:9
[INFO] [stdout]     |
[INFO] [stdout]  96 | pub struct Variant {
[INFO] [stdout]     |            ------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 114 |     pub ref_motif: String,
[INFO] [stdout]     |         ^^^^^^^^^
[INFO] [stdout] 115 |     /// Reference sequence
[INFO] [stdout] 116 |     pub ref_seq: String,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `Variant` 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 `complement_spans` is never used
[INFO] [stdout]   --> src/utils/mod.rs:72:8
[INFO] [stdout]    |
[INFO] [stdout] 72 | pub fn complement_spans(spans: &[(i32, i32)], _min: i32, _max: i32) -> Vec<(i32, i32)> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `create_temp_file` is never used
[INFO] [stdout]    --> src/utils/mod.rs:111:8
[INFO] [stdout]     |
[INFO] [stdout] 111 | pub fn create_temp_file(content: &str, _suffix: &str) -> std::io::Result<NamedTempFile> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_bed_line` is never used
[INFO] [stdout]    --> src/utils/mod.rs:118:8
[INFO] [stdout]     |
[INFO] [stdout] 118 | pub fn parse_bed_line(line: &str) -> Option<(String, i32, i32, Option<String>)> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `read_bed_file` is never used
[INFO] [stdout]    --> src/utils/mod.rs:133:8
[INFO] [stdout]     |
[INFO] [stdout] 133 | pub fn read_bed_file<P: AsRef<Path>>(path: P) -> std::io::Result<Vec<(String, i32, i32, Option<String>)>> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 01s
[INFO] running `Command { std: "docker" "inspect" "54b12e7e858d694393d8d7f42751345444099740da2c3e81c2042bc91939ec67", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "54b12e7e858d694393d8d7f42751345444099740da2c3e81c2042bc91939ec67", kill_on_drop: false }`
[INFO] [stdout] 54b12e7e858d694393d8d7f42751345444099740da2c3e81c2042bc91939ec67
