[INFO] crate fasten 0.1.13 is already in cache
[INFO] extracting crate fasten 0.1.13 into work/ex/clippy-test-run/sources/stable/reg/fasten/0.1.13
[INFO] extracting crate fasten 0.1.13 into work/ex/clippy-test-run/sources/stable+rustflags=-Dclippy%3A%3Ainto_iter_on_array/reg/fasten/0.1.13
[INFO] validating manifest of fasten-0.1.13 on toolchain stable
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "read-manifest" "--manifest-path" "Cargo.toml"`
[INFO] validating manifest of fasten-0.1.13 on toolchain stable+rustflags=-Dclippy::into_iter_on_array
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "read-manifest" "--manifest-path" "Cargo.toml"`
[INFO] started frobbing fasten-0.1.13
[INFO] finished frobbing fasten-0.1.13
[INFO] frobbed toml for fasten-0.1.13 written to work/ex/clippy-test-run/sources/stable/reg/fasten/0.1.13/Cargo.toml
[INFO] started frobbing fasten-0.1.13
[INFO] finished frobbing fasten-0.1.13
[INFO] frobbed toml for fasten-0.1.13 written to work/ex/clippy-test-run/sources/stable+rustflags=-Dclippy%3A%3Ainto_iter_on_array/reg/fasten/0.1.13/Cargo.toml
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"`
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update"`
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] running `"/mnt/big/crater/work/local/cargo-home/bin/cargo" "+stable" "fetch" "--locked" "--manifest-path" "Cargo.toml"`
[INFO] linting fasten-0.1.13 against stable for clippy-test-run
[INFO] running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/clippy-test-run/worker-7/stable:/opt/crater/target:rw,Z" "-v" "/mnt/big/crater/work/ex/clippy-test-run/sources/stable/reg/fasten/0.1.13:/opt/crater/workdir:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/opt/crater/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/opt/crater/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/opt/crater/workdir" "-e" "MAP_USER_ID=1000" "-e" "CARGO_TARGET_DIR=/opt/crater/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/crater/cargo-home" "-e" "RUSTUP_HOME=/opt/crater/rustup-home" "-w" "/opt/crater/workdir" "-m" "1536M" "--network" "none" "rustops/crates-build-env" "/opt/crater/cargo-home/bin/cargo" "+stable" "clippy" "--frozen" "--all" "--all-targets"`
[INFO] [stdout] e23ecc15233c93006e1ae1d79dec0c7cee54e571b7ada1bf0ced9f5f4f559723
[INFO] running `"docker" "start" "-a" "e23ecc15233c93006e1ae1d79dec0c7cee54e571b7ada1bf0ced9f5f4f559723"`
[INFO] [stderr]     Checking multiqueue v0.3.2
[INFO] [stderr]     Checking statistical v0.1.1
[INFO] [stderr]     Checking fasten v0.1.13 (/opt/crater/workdir)
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]   --> src/io/seq.rs:76:13
[INFO] [stderr]    |
[INFO] [stderr] 76 |             thresholds: thresholds,
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^ help: replace it with: `thresholds`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::redundant_field_names)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: redundant field names in struct initialization
[INFO] [stderr]   --> src/io/seq.rs:76:13
[INFO] [stderr]    |
[INFO] [stderr] 76 |             thresholds: thresholds,
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^ help: replace it with: `thresholds`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::redundant_field_names)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#redundant_field_names
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/io/fastq.rs:91:13
[INFO] [stderr]    |
[INFO] [stderr] 91 |             return Some(seq)
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Some(seq)`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/fastq.rs:168:13
[INFO] [stderr]     |
[INFO] [stderr] 168 |             return Some(seq)
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Some(seq)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/io/seq.rs:71:9
[INFO] [stderr]    |
[INFO] [stderr] 71 | /         return Seq{
[INFO] [stderr] 72 | |             id:     id_copy,
[INFO] [stderr] 73 | |             seq:    seq.clone(),
[INFO] [stderr] 74 | |             qual:   qual.clone(),
[INFO] [stderr] 75 | |             pairid: String::new(),
[INFO] [stderr] 76 | |             thresholds: thresholds,
[INFO] [stderr] 77 | |         };
[INFO] [stderr]    | |__________^
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]    |
[INFO] [stderr] 71 |         Seq{
[INFO] [stderr] 72 |             id:     id_copy,
[INFO] [stderr] 73 |             seq:    seq.clone(),
[INFO] [stderr] 74 |             qual:   qual.clone(),
[INFO] [stderr] 75 |             pairid: String::new(),
[INFO] [stderr] 76 |             thresholds: thresholds,
[INFO] [stderr]  ...
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/io/seq.rs:81:9
[INFO] [stderr]    |
[INFO] [stderr] 81 |         return Seq::new(&String::new(),&String::new(),&String::new());
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Seq::new(&String::new(),&String::new(),&String::new())`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/io/seq.rs:88:9
[INFO] [stderr]    |
[INFO] [stderr] 88 |         return false;
[INFO] [stderr]    |         ^^^^^^^^^^^^^ help: remove `return` as shown: `false`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/seq.rs:105:9
[INFO] [stderr]     |
[INFO] [stderr] 105 | /         return Seq{
[INFO] [stderr] 106 | |             id:       id.to_string(),
[INFO] [stderr] 107 | |             seq:      seq.to_string(),
[INFO] [stderr] 108 | |             qual:     qual.to_string(),
[INFO] [stderr] 109 | |             pairid:   String::new(),
[INFO] [stderr] 110 | |             thresholds: HashMap::new(),
[INFO] [stderr] 111 | |         }
[INFO] [stderr]     | |_________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]     |
[INFO] [stderr] 105 |         Seq{
[INFO] [stderr] 106 |             id:       id.to_string(),
[INFO] [stderr] 107 |             seq:      seq.to_string(),
[INFO] [stderr] 108 |             qual:     qual.to_string(),
[INFO] [stderr] 109 |             pairid:   String::new(),
[INFO] [stderr] 110 |             thresholds: HashMap::new(),
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/seq.rs:124:9
[INFO] [stderr]     |
[INFO] [stderr] 124 |         return id_copy;
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^ help: remove `return` as shown: `id_copy`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/seq.rs:215:9
[INFO] [stderr]     |
[INFO] [stderr] 215 |         return true;
[INFO] [stderr]     |         ^^^^^^^^^^^^ help: remove `return` as shown: `true`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/seq.rs:228:9
[INFO] [stderr]     |
[INFO] [stderr] 228 |         return entry;
[INFO] [stderr]     |         ^^^^^^^^^^^^^ help: remove `return` as shown: `entry`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]    --> src/io/seq.rs:230:21
[INFO] [stderr]     |
[INFO] [stderr] 230 |     fn print(&self) -> () {
[INFO] [stderr]     |                     ^^^^^ help: remove the `-> ()`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::unused_unit)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/seq.rs:237:9
[INFO] [stderr]     |
[INFO] [stderr] 237 | /         return Seq{
[INFO] [stderr] 238 | |             id:     self.id.clone(),
[INFO] [stderr] 239 | |             seq:    self.seq.clone(),
[INFO] [stderr] 240 | |             qual:   self.qual.clone(),
[INFO] [stderr] 241 | |             pairid: self.pairid.clone(),
[INFO] [stderr] 242 | |             thresholds: self.thresholds.clone(),
[INFO] [stderr] 243 | |         }
[INFO] [stderr]     | |_________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]     |
[INFO] [stderr] 237 |         Seq{
[INFO] [stderr] 238 |             id:     self.id.clone(),
[INFO] [stderr] 239 |             seq:    self.seq.clone(),
[INFO] [stderr] 240 |             qual:   self.qual.clone(),
[INFO] [stderr] 241 |             pairid: self.pairid.clone(),
[INFO] [stderr] 242 |             thresholds: self.thresholds.clone(),
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]   --> src/lib.rs:24:16
[INFO] [stderr]    |
[INFO] [stderr] 24 | pub fn eexit() -> () {
[INFO] [stderr]    |                ^^^^^ help: remove the `-> ()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/lib.rs:54:5
[INFO] [stderr]    |
[INFO] [stderr] 54 |     return opts;
[INFO] [stderr]    |     ^^^^^^^^^^^^ help: remove `return` as shown: `opts`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]   --> src/io/seq.rs:41:17
[INFO] [stderr]    |
[INFO] [stderr] 41 |     fn new (id: &String, seq: &String, qual: &String) -> Seq;
[INFO] [stderr]    |                 ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]   --> src/io/seq.rs:41:31
[INFO] [stderr]    |
[INFO] [stderr] 41 |     fn new (id: &String, seq: &String, qual: &String) -> Seq;
[INFO] [stderr]    |                               ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]   --> src/io/seq.rs:41:46
[INFO] [stderr]    |
[INFO] [stderr] 41 |     fn new (id: &String, seq: &String, qual: &String) -> Seq;
[INFO] [stderr]    |                                              ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]   --> src/io/seq.rs:47:30
[INFO] [stderr]    |
[INFO] [stderr] 47 |     fn from_string (seq_str: &String) -> Seq;
[INFO] [stderr]    |                              ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]   --> src/io/seq.rs:49:24
[INFO] [stderr]    |
[INFO] [stderr] 49 |     fn sanitize_id(id: &String) -> (String);
[INFO] [stderr]    |                        ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/io/seq.rs:85:12
[INFO] [stderr]    |
[INFO] [stderr] 85 |         if self.seq.len() == 0 && self.qual.len() == 0 {
[INFO] [stderr]    |            ^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `self.seq.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::len_zero)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/io/seq.rs:85:35
[INFO] [stderr]    |
[INFO] [stderr] 85 |         if self.seq.len() == 0 && self.qual.len() == 0 {
[INFO] [stderr]    |                                   ^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `self.qual.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/io/seq.rs:117:12
[INFO] [stderr]     |
[INFO] [stderr] 117 |         if id.len() == 0 {
[INFO] [stderr]     |            ^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `id.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: the operation is ineffective. Consider reducing it to `33`
[INFO] [stderr]    --> src/io/seq.rs:131:32
[INFO] [stderr]     |
[INFO] [stderr] 131 |         let low_score :char  = (33 + 0) as u8 as char;
[INFO] [stderr]     |                                ^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::identity_op)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#identity_op
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/io/seq.rs:150:46
[INFO] [stderr]     |
[INFO] [stderr] 150 |                 new_qual.push_str(&self.qual[i..i+1]);
[INFO] [stderr]     |                                              ^^^^^^ help: use: `i..=i`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::range_plus_one)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: the operation is ineffective. Consider reducing it to `&self.qual.len()`
[INFO] [stderr]    --> src/io/seq.rs:164:23
[INFO] [stderr]     |
[INFO] [stderr] 164 |         let mut trim3=&self.qual.len()-0;
[INFO] [stderr]     |                       ^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#identity_op
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/io/seq.rs:220:12
[INFO] [stderr]     |
[INFO] [stderr] 220 |         if self.id.len() > 0 && self.id.chars().nth(0).expect("Seq ID was not set") != '@' {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!self.id.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/io/fastq.rs:91:13
[INFO] [stderr]    |
[INFO] [stderr] 91 |             return Some(seq)
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Some(seq)`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/fastq.rs:168:13
[INFO] [stderr]     |
[INFO] [stderr] 168 |             return Some(seq)
[INFO] [stderr]     |             ^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Some(seq)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/io/seq.rs:71:9
[INFO] [stderr]    |
[INFO] [stderr] 71 | /         return Seq{
[INFO] [stderr] 72 | |             id:     id_copy,
[INFO] [stderr] 73 | |             seq:    seq.clone(),
[INFO] [stderr] 74 | |             qual:   qual.clone(),
[INFO] [stderr] 75 | |             pairid: String::new(),
[INFO] [stderr] 76 | |             thresholds: thresholds,
[INFO] [stderr] 77 | |         };
[INFO] [stderr]    | |__________^
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]    |
[INFO] [stderr] 71 |         Seq{
[INFO] [stderr] 72 |             id:     id_copy,
[INFO] [stderr] 73 |             seq:    seq.clone(),
[INFO] [stderr] 74 |             qual:   qual.clone(),
[INFO] [stderr] 75 |             pairid: String::new(),
[INFO] [stderr] 76 |             thresholds: thresholds,
[INFO] [stderr]  ...
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/io/seq.rs:81:9
[INFO] [stderr]    |
[INFO] [stderr] 81 |         return Seq::new(&String::new(),&String::new(),&String::new());
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `Seq::new(&String::new(),&String::new(),&String::new())`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/io/seq.rs:88:9
[INFO] [stderr]    |
[INFO] [stderr] 88 |         return false;
[INFO] [stderr]    |         ^^^^^^^^^^^^^ help: remove `return` as shown: `false`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/seq.rs:105:9
[INFO] [stderr]     |
[INFO] [stderr] 105 | /         return Seq{
[INFO] [stderr] 106 | |             id:       id.to_string(),
[INFO] [stderr] 107 | |             seq:      seq.to_string(),
[INFO] [stderr] 108 | |             qual:     qual.to_string(),
[INFO] [stderr] 109 | |             pairid:   String::new(),
[INFO] [stderr] 110 | |             thresholds: HashMap::new(),
[INFO] [stderr] 111 | |         }
[INFO] [stderr]     | |_________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]     |
[INFO] [stderr] 105 |         Seq{
[INFO] [stderr] 106 |             id:       id.to_string(),
[INFO] [stderr] 107 |             seq:      seq.to_string(),
[INFO] [stderr] 108 |             qual:     qual.to_string(),
[INFO] [stderr] 109 |             pairid:   String::new(),
[INFO] [stderr] 110 |             thresholds: HashMap::new(),
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/seq.rs:124:9
[INFO] [stderr]     |
[INFO] [stderr] 124 |         return id_copy;
[INFO] [stderr]     |         ^^^^^^^^^^^^^^^ help: remove `return` as shown: `id_copy`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/seq.rs:215:9
[INFO] [stderr]     |
[INFO] [stderr] 215 |         return true;
[INFO] [stderr]     |         ^^^^^^^^^^^^ help: remove `return` as shown: `true`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/seq.rs:228:9
[INFO] [stderr]     |
[INFO] [stderr] 228 |         return entry;
[INFO] [stderr]     |         ^^^^^^^^^^^^^ help: remove `return` as shown: `entry`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]    --> src/io/seq.rs:230:21
[INFO] [stderr]     |
[INFO] [stderr] 230 |     fn print(&self) -> () {
[INFO] [stderr]     |                     ^^^^^ help: remove the `-> ()`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::unused_unit)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/io/seq.rs:237:9
[INFO] [stderr]     |
[INFO] [stderr] 237 | /         return Seq{
[INFO] [stderr] 238 | |             id:     self.id.clone(),
[INFO] [stderr] 239 | |             seq:    self.seq.clone(),
[INFO] [stderr] 240 | |             qual:   self.qual.clone(),
[INFO] [stderr] 241 | |             pairid: self.pairid.clone(),
[INFO] [stderr] 242 | |             thresholds: self.thresholds.clone(),
[INFO] [stderr] 243 | |         }
[INFO] [stderr]     | |_________^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] help: remove `return` as shown
[INFO] [stderr]     |
[INFO] [stderr] 237 |         Seq{
[INFO] [stderr] 238 |             id:     self.id.clone(),
[INFO] [stderr] 239 |             seq:    self.seq.clone(),
[INFO] [stderr] 240 |             qual:   self.qual.clone(),
[INFO] [stderr] 241 |             pairid: self.pairid.clone(),
[INFO] [stderr] 242 |             thresholds: self.thresholds.clone(),
[INFO] [stderr]   ...
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]   --> src/lib.rs:24:16
[INFO] [stderr]    |
[INFO] [stderr] 24 | pub fn eexit() -> () {
[INFO] [stderr]    |                ^^^^^ help: remove the `-> ()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]   --> src/lib.rs:54:5
[INFO] [stderr]    |
[INFO] [stderr] 54 |     return opts;
[INFO] [stderr]    |     ^^^^^^^^^^^^ help: remove `return` as shown: `opts`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: using `write!()` with a format string that ends in a single newline, consider using `writeln!()` instead
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:65:13
[INFO] [stderr]    |
[INFO] [stderr] 65 |             write!(file1,"{}\n",seq.to_string()).unwrap();
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::write_with_newline)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#write_with_newline
[INFO] [stderr] 
[INFO] [stderr] warning: using `write!()` with a format string that ends in a single newline, consider using `writeln!()` instead
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:67:13
[INFO] [stderr]    |
[INFO] [stderr] 67 |             write!(file2,"{}\n",seq.to_string()).unwrap();
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#write_with_newline
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]   --> src/io/seq.rs:41:17
[INFO] [stderr]    |
[INFO] [stderr] 41 |     fn new (id: &String, seq: &String, qual: &String) -> Seq;
[INFO] [stderr]    |                 ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]   --> src/io/seq.rs:41:31
[INFO] [stderr]    |
[INFO] [stderr] 41 |     fn new (id: &String, seq: &String, qual: &String) -> Seq;
[INFO] [stderr]    |                               ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]   --> src/io/seq.rs:41:46
[INFO] [stderr]    |
[INFO] [stderr] 41 |     fn new (id: &String, seq: &String, qual: &String) -> Seq;
[INFO] [stderr]    |                                              ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]   --> src/io/seq.rs:47:30
[INFO] [stderr]    |
[INFO] [stderr] 47 |     fn from_string (seq_str: &String) -> Seq;
[INFO] [stderr]    |                              ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]   --> src/io/seq.rs:49:24
[INFO] [stderr]    |
[INFO] [stderr] 49 |     fn sanitize_id(id: &String) -> (String);
[INFO] [stderr]    |                        ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/io/seq.rs:85:12
[INFO] [stderr]    |
[INFO] [stderr] 85 |         if self.seq.len() == 0 && self.qual.len() == 0 {
[INFO] [stderr]    |            ^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `self.seq.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::len_zero)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/io/seq.rs:85:35
[INFO] [stderr]    |
[INFO] [stderr] 85 |         if self.seq.len() == 0 && self.qual.len() == 0 {
[INFO] [stderr]    |                                   ^^^^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `self.qual.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/io/seq.rs:117:12
[INFO] [stderr]     |
[INFO] [stderr] 117 |         if id.len() == 0 {
[INFO] [stderr]     |            ^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `id.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: the operation is ineffective. Consider reducing it to `33`
[INFO] [stderr]    --> src/io/seq.rs:131:32
[INFO] [stderr]     |
[INFO] [stderr] 131 |         let low_score :char  = (33 + 0) as u8 as char;
[INFO] [stderr]     |                                ^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::identity_op)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#identity_op
[INFO] [stderr] 
[INFO] [stderr] warning: an inclusive range would be more readable
[INFO] [stderr]    --> src/io/seq.rs:150:46
[INFO] [stderr]     |
[INFO] [stderr] 150 |                 new_qual.push_str(&self.qual[i..i+1]);
[INFO] [stderr]     |                                              ^^^^^^ help: use: `i..=i`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::range_plus_one)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#range_plus_one
[INFO] [stderr] 
[INFO] [stderr] warning: the operation is ineffective. Consider reducing it to `&self.qual.len()`
[INFO] [stderr]    --> src/io/seq.rs:164:23
[INFO] [stderr]     |
[INFO] [stderr] 164 |         let mut trim3=&self.qual.len()-0;
[INFO] [stderr]     |                       ^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#identity_op
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]    --> src/io/seq.rs:220:12
[INFO] [stderr]     |
[INFO] [stderr] 220 |         if self.id.len() > 0 && self.id.chars().nth(0).expect("Seq ID was not set") != '@' {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `!self.id.is_empty()`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_pe.rs:131:5
[INFO] [stderr]     |
[INFO] [stderr] 131 |     return 1;
[INFO] [stderr]     |     ^^^^^^^^^ help: remove `return` as shown: `1`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_pe.rs:166:5
[INFO] [stderr]     |
[INFO] [stderr] 166 |     return 1;
[INFO] [stderr]     |     ^^^^^^^^^ help: remove `return` as shown: `1`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]   --> src/bin/fasten_pe.rs:93:35
[INFO] [stderr]    |
[INFO] [stderr] 93 | fn is_paired_end_slash12(id1_ref: &Vec<String>, id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]    |                                   ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] help: change this to
[INFO] [stderr]    |
[INFO] [stderr] 93 | fn is_paired_end_slash12(id1_ref: &[String], id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]    |                                   ^^^^^^^^^
[INFO] [stderr] help: change `id1_ref.clone()` to
[INFO] [stderr]    |
[INFO] [stderr] 96 |     let id1_vec = id1_ref.to_owned();
[INFO] [stderr]    |                   ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]   --> src/bin/fasten_pe.rs:93:58
[INFO] [stderr]    |
[INFO] [stderr] 93 | fn is_paired_end_slash12(id1_ref: &Vec<String>, id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]    |                                                          ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] help: change this to
[INFO] [stderr]    |
[INFO] [stderr] 93 | fn is_paired_end_slash12(id1_ref: &Vec<String>, id2_ref: &[String]) -> u8 {
[INFO] [stderr]    |                                                          ^^^^^^^^^
[INFO] [stderr] help: change `id2_ref.clone()` to
[INFO] [stderr]    |
[INFO] [stderr] 97 |     let id2_vec = id2_ref.to_owned();
[INFO] [stderr]    |                   ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/bin/fasten_pe.rs:135:33
[INFO] [stderr]     |
[INFO] [stderr] 135 | fn is_paired_end_miseq(id1_ref: &Vec<String>, id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]     |                                 ^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] help: change this to
[INFO] [stderr]     |
[INFO] [stderr] 135 | fn is_paired_end_miseq(id1_ref: &[String], id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]     |                                 ^^^^^^^^^
[INFO] [stderr] help: change `id1_ref.clone()` to
[INFO] [stderr]     |
[INFO] [stderr] 137 |     let id1_vec = id1_ref.to_owned();
[INFO] [stderr]     |                   ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/bin/fasten_pe.rs:135:56
[INFO] [stderr]     |
[INFO] [stderr] 135 | fn is_paired_end_miseq(id1_ref: &Vec<String>, id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]     |                                                        ^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] help: change this to
[INFO] [stderr]     |
[INFO] [stderr] 135 | fn is_paired_end_miseq(id1_ref: &Vec<String>, id2_ref: &[String]) -> u8 {
[INFO] [stderr]     |                                                        ^^^^^^^^^
[INFO] [stderr] help: change `id2_ref.clone()` to
[INFO] [stderr]     |
[INFO] [stderr] 138 |     let id2_vec = id2_ref.to_owned();
[INFO] [stderr]     |                   ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: single-character string constant used as pattern
[INFO] [stderr]    --> src/bin/fasten_pe.rs:149:33
[INFO] [stderr]     |
[INFO] [stderr] 149 |         let id1_tmp = id1.split(":").nth(6);
[INFO] [stderr]     |                                 ^^^ help: try using a char instead: `':'`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::single_char_pattern)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern
[INFO] [stderr] 
[INFO] [stderr] warning: single-character string constant used as pattern
[INFO] [stderr]    --> src/bin/fasten_pe.rs:150:33
[INFO] [stderr]     |
[INFO] [stderr] 150 |         let id2_tmp = id2.split(":").nth(6);
[INFO] [stderr]     |                                 ^^^ help: try using a char instead: `':'`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern
[INFO] [stderr] 
[INFO] [stderr] warning: single-character string constant used as pattern
[INFO] [stderr]    --> src/bin/fasten_pe.rs:156:54
[INFO] [stderr]     |
[INFO] [stderr] 156 |         let id1_read_number = id1_tmp.unwrap().split(" ").nth(1);
[INFO] [stderr]     |                                                      ^^^ help: try using a char instead: `' '`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern
[INFO] [stderr] 
[INFO] [stderr] warning: single-character string constant used as pattern
[INFO] [stderr]    --> src/bin/fasten_pe.rs:157:54
[INFO] [stderr]     |
[INFO] [stderr] 157 |         let id2_read_number = id2_tmp.unwrap().split(" ").nth(1);
[INFO] [stderr]     |                                                      ^^^ help: try using a char instead: `' '`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `num_lines` is used as a loop counter. Consider using `for (num_lines, item) in my_buffer.lines().enumerate()` or similar iterators
[INFO] [stderr]   --> src/bin/fasten_trim.rs:60:17
[INFO] [stderr]    |
[INFO] [stderr] 60 |     for line in my_buffer.lines() {
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:39:42
[INFO] [stderr]    |
[INFO] [stderr] 39 | fn deshuffle(matches: &getopts::Matches) -> () {
[INFO] [stderr]    |                                          ^^^^^ help: remove the `-> ()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::unused_unit)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:74:40
[INFO] [stderr]    |
[INFO] [stderr] 74 | fn shuffle(matches: &getopts::Matches) -> () {
[INFO] [stderr]    |                                        ^^^^^ help: remove the `-> ()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_shuffle.rs:117:5
[INFO] [stderr]     |
[INFO] [stderr] 117 |     return seqs;
[INFO] [stderr]     |     ^^^^^^^^^^^^ help: remove `return` as shown: `seqs`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `read_counter` is used as a loop counter. Consider using `for (read_counter, item) in fastq_reader.enumerate()` or similar iterators
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:61:16
[INFO] [stderr]    |
[INFO] [stderr] 61 |     for seq in fastq_reader {
[INFO] [stderr]    |                ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:97:8
[INFO] [stderr]    |
[INFO] [stderr] 97 |     if seqs2.len() == 0 {
[INFO] [stderr]    |        ^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `seqs2.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::len_zero)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/bin/fasten_shuffle.rs:111:24
[INFO] [stderr]     |
[INFO] [stderr] 111 | fn read_seqs(filename: &String) -> Vec<Seq> {
[INFO] [stderr]     |                        ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `line_counter` is used as a loop counter. Consider using `for (line_counter, item) in my_buffer.lines().enumerate()` or similar iterators
[INFO] [stderr]   --> src/bin/fasten_sample.rs:54:17
[INFO] [stderr]    |
[INFO] [stderr] 54 |     for line in my_buffer.lines() {
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_metrics.rs:137:5
[INFO] [stderr]     |
[INFO] [stderr] 137 |     return avg_square_diff.sqrt();
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `avg_square_diff.sqrt()`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to u32 may become silently lossy if types change
[INFO] [stderr]   --> src/bin/fasten_metrics.rs:80:37
[INFO] [stderr]    |
[INFO] [stderr] 80 |                     my_read_qual += qual_char as u8 as u32 - 33;
[INFO] [stderr]    |                                     ^^^^^^^^^^^^^^^^^^^^^^ help: try: `u32::from(qual_char as u8)`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::cast_lossless)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/bin/fasten_metrics.rs:125:28
[INFO] [stderr]     |
[INFO] [stderr] 125 | fn standard_deviation(vec :&Vec<f32>) -> f32{
[INFO] [stderr]     |                            ^^^^^^^^^ help: change this to: `&[f32]`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]   --> src/bin/fasten_randomize.rs:35:48
[INFO] [stderr]    |
[INFO] [stderr] 35 | fn print_reads_from_stdin(lines_per_read :u32) -> () {
[INFO] [stderr]    |                                                ^^^^^ help: remove the `-> ()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::unused_unit)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: long literal lacking separators
[INFO] [stderr]   --> src/bin/fasten_randomize.rs:37:52
[INFO] [stderr]    |
[INFO] [stderr] 37 |     let mut seqs :Vec<String> = Vec::with_capacity(100000);
[INFO] [stderr]    |                                                    ^^^^^^ help: consider: `100_000`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::unreadable_literal)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unreadable_literal
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_combine.rs:106:17
[INFO] [stderr]     |
[INFO] [stderr] 106 |                 return p;
[INFO] [stderr]     |                 ^^^^^^^^^ help: remove `return` as shown: `p`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_combine.rs:171:5
[INFO] [stderr]     |
[INFO] [stderr] 171 |     return new_errors;
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `new_errors`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_combine.rs:209:5
[INFO] [stderr]     |
[INFO] [stderr] 209 |     return qual_out;
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^ help: remove `return` as shown: `qual_out`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to f32 may become silently lossy if types change
[INFO] [stderr]   --> src/bin/fasten_combine.rs:92:32
[INFO] [stderr]    |
[INFO] [stderr] 92 |                 let qual_int = qual_char as u8 as f32 - 33.0;
[INFO] [stderr]    |                                ^^^^^^^^^^^^^^^^^^^^^^ help: try: `f32::from(qual_char as u8)`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::cast_lossless)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: use of `or_insert` followed by a function call
[INFO] [stderr]    --> src/bin/fasten_combine.rs:101:66
[INFO] [stderr]     |
[INFO] [stderr] 101 |             let qual_vec = seq_error_rate.entry(seq_key.clone()).or_insert(Vec::new());
[INFO] [stderr]     |                                                                  ^^^^^^^^^^^^^^^^^^^^^ help: try this: `or_insert_with(Vec::new)`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::or_fun_call)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#or_fun_call
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to f32 may become silently lossy if types change
[INFO] [stderr]    --> src/bin/fasten_combine.rs:104:32
[INFO] [stderr]     |
[INFO] [stderr] 104 |                 let qual_int = qual_char as u8 as f32 - 33.0;
[INFO] [stderr]     |                                ^^^^^^^^^^^^^^^^^^^^^^ help: try: `f32::from(qual_char as u8)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `seq_counter` is used as a loop counter. Consider using `for (seq_counter, item) in seq_error_rate.enumerate()` or similar iterators
[INFO] [stderr]    --> src/bin/fasten_combine.rs:119:32
[INFO] [stderr]     |
[INFO] [stderr] 119 |     for (seq,combined_qual) in seq_error_rate {
[INFO] [stderr]     |                                ^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to f32 may become silently lossy if types change
[INFO] [stderr]    --> src/bin/fasten_combine.rs:129:59
[INFO] [stderr]     |
[INFO] [stderr] 129 |             if qual_recalc.is_infinite() || qual_recalc > max_qual as f32 {
[INFO] [stderr]     |                                                           ^^^^^^^^^^^^^^^ help: try: `f32::from(max_qual)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to f32 may become silently lossy if types change
[INFO] [stderr]    --> src/bin/fasten_combine.rs:130:31
[INFO] [stderr]     |
[INFO] [stderr] 130 |                 qual_recalc = max_qual as f32;
[INFO] [stderr]     |                               ^^^^^^^^^^^^^^^ help: try: `f32::from(max_qual)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/bin/fasten_combine.rs:161:35
[INFO] [stderr]     |
[INFO] [stderr] 161 | fn combine_error_vectors(errors1 :&Vec<f32>, errors2: &Vec<f32>) -> Vec<f32> {
[INFO] [stderr]     |                                   ^^^^^^^^^ help: change this to: `&[f32]`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/bin/fasten_combine.rs:161:55
[INFO] [stderr]     |
[INFO] [stderr] 161 | fn combine_error_vectors(errors1 :&Vec<f32>, errors2: &Vec<f32>) -> Vec<f32> {
[INFO] [stderr]     |                                                       ^^^^^^^^^ help: change this to: `&[f32]`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: casting character literal to u8. `char`s are 4 bytes wide in rust, so casting to u8 truncates them
[INFO] [stderr]    --> src/bin/fasten_combine.rs:182:20
[INFO] [stderr]     |
[INFO] [stderr] 182 |     let max_qual = 'I' as u8;
[INFO] [stderr]     |                    ^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::char_lit_as_u8)] on by default
[INFO] [stderr]     = help: Consider using a byte literal instead:
[INFO] [stderr]             b'I'
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#char_lit_as_u8
[INFO] [stderr] 
[INFO] [stderr] warning: casting character literal to u8. `char`s are 4 bytes wide in rust, so casting to u8 truncates them
[INFO] [stderr]    --> src/bin/fasten_combine.rs:183:20
[INFO] [stderr]     |
[INFO] [stderr] 183 |     let min_qual = '!' as u8;
[INFO] [stderr]     |                    ^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: Consider using a byte literal instead:
[INFO] [stderr]             b'!'
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#char_lit_as_u8
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to f32 may become silently lossy if types change
[INFO] [stderr]    --> src/bin/fasten_combine.rs:187:24
[INFO] [stderr]     |
[INFO] [stderr] 187 |         let qual_int = qual_char as u8 as f32 - 33.0;
[INFO] [stderr]     |                        ^^^^^^^^^^^^^^^^^^^^^^ help: try: `f32::from(qual_char as u8)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_combine.rs:106:17
[INFO] [stderr]     |
[INFO] [stderr] 106 |                 return p;
[INFO] [stderr]     |                 ^^^^^^^^^ help: remove `return` as shown: `p`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_combine.rs:171:5
[INFO] [stderr]     |
[INFO] [stderr] 171 |     return new_errors;
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `new_errors`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_combine.rs:209:5
[INFO] [stderr]     |
[INFO] [stderr] 209 |     return qual_out;
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^ help: remove `return` as shown: `qual_out`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to f32 may become silently lossy if types change
[INFO] [stderr]   --> src/bin/fasten_combine.rs:92:32
[INFO] [stderr]    |
[INFO] [stderr] 92 |                 let qual_int = qual_char as u8 as f32 - 33.0;
[INFO] [stderr]    |                                ^^^^^^^^^^^^^^^^^^^^^^ help: try: `f32::from(qual_char as u8)`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::cast_lossless)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: use of `or_insert` followed by a function call
[INFO] [stderr]    --> src/bin/fasten_combine.rs:101:66
[INFO] [stderr]     |
[INFO] [stderr] 101 |             let qual_vec = seq_error_rate.entry(seq_key.clone()).or_insert(Vec::new());
[INFO] [stderr]     |                                                                  ^^^^^^^^^^^^^^^^^^^^^ help: try this: `or_insert_with(Vec::new)`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::or_fun_call)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#or_fun_call
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to f32 may become silently lossy if types change
[INFO] [stderr]    --> src/bin/fasten_combine.rs:104:32
[INFO] [stderr]     |
[INFO] [stderr] 104 |                 let qual_int = qual_char as u8 as f32 - 33.0;
[INFO] [stderr]     |                                ^^^^^^^^^^^^^^^^^^^^^^ help: try: `f32::from(qual_char as u8)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `seq_counter` is used as a loop counter. Consider using `for (seq_counter, item) in seq_error_rate.enumerate()` or similar iterators
[INFO] [stderr]    --> src/bin/fasten_combine.rs:119:32
[INFO] [stderr]     |
[INFO] [stderr] 119 |     for (seq,combined_qual) in seq_error_rate {
[INFO] [stderr]     |                                ^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to f32 may become silently lossy if types change
[INFO] [stderr]    --> src/bin/fasten_combine.rs:129:59
[INFO] [stderr]     |
[INFO] [stderr] 129 |             if qual_recalc.is_infinite() || qual_recalc > max_qual as f32 {
[INFO] [stderr]     |                                                           ^^^^^^^^^^^^^^^ help: try: `f32::from(max_qual)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to f32 may become silently lossy if types change
[INFO] [stderr]    --> src/bin/fasten_combine.rs:130:31
[INFO] [stderr]     |
[INFO] [stderr] 130 |                 qual_recalc = max_qual as f32;
[INFO] [stderr]     |                               ^^^^^^^^^^^^^^^ help: try: `f32::from(max_qual)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/bin/fasten_combine.rs:161:35
[INFO] [stderr]     |
[INFO] [stderr] 161 | fn combine_error_vectors(errors1 :&Vec<f32>, errors2: &Vec<f32>) -> Vec<f32> {
[INFO] [stderr]     |                                   ^^^^^^^^^ help: change this to: `&[f32]`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/bin/fasten_combine.rs:161:55
[INFO] [stderr]     |
[INFO] [stderr] 161 | fn combine_error_vectors(errors1 :&Vec<f32>, errors2: &Vec<f32>) -> Vec<f32> {
[INFO] [stderr]     |                                                       ^^^^^^^^^ help: change this to: `&[f32]`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: casting character literal to u8. `char`s are 4 bytes wide in rust, so casting to u8 truncates them
[INFO] [stderr]    --> src/bin/fasten_combine.rs:182:20
[INFO] [stderr]     |
[INFO] [stderr] 182 |     let max_qual = 'I' as u8;
[INFO] [stderr]     |                    ^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::char_lit_as_u8)] on by default
[INFO] [stderr]     = help: Consider using a byte literal instead:
[INFO] [stderr]             b'I'
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#char_lit_as_u8
[INFO] [stderr] 
[INFO] [stderr] warning: casting character literal to u8. `char`s are 4 bytes wide in rust, so casting to u8 truncates them
[INFO] [stderr]    --> src/bin/fasten_combine.rs:183:20
[INFO] [stderr]     |
[INFO] [stderr] 183 |     let min_qual = '!' as u8;
[INFO] [stderr]     |                    ^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: Consider using a byte literal instead:
[INFO] [stderr]             b'!'
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#char_lit_as_u8
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to f32 may become silently lossy if types change
[INFO] [stderr]    --> src/bin/fasten_combine.rs:187:24
[INFO] [stderr]     |
[INFO] [stderr] 187 |         let qual_int = qual_char as u8 as f32 - 33.0;
[INFO] [stderr]     |                        ^^^^^^^^^^^^^^^^^^^^^^ help: try: `f32::from(qual_char as u8)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `num_lines` is used as a loop counter. Consider using `for (num_lines, item) in my_buffer.lines().enumerate()` or similar iterators
[INFO] [stderr]   --> src/bin/fasten_quality_filter.rs:52:17
[INFO] [stderr]    |
[INFO] [stderr] 52 |     for line in my_buffer.lines() {
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_metrics.rs:137:5
[INFO] [stderr]     |
[INFO] [stderr] 137 |     return avg_square_diff.sqrt();
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `avg_square_diff.sqrt()`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to u32 may become silently lossy if types change
[INFO] [stderr]   --> src/bin/fasten_metrics.rs:80:37
[INFO] [stderr]    |
[INFO] [stderr] 80 |                     my_read_qual += qual_char as u8 as u32 - 33;
[INFO] [stderr]    |                                     ^^^^^^^^^^^^^^^^^^^^^^ help: try: `u32::from(qual_char as u8)`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::cast_lossless)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/bin/fasten_metrics.rs:125:28
[INFO] [stderr]     |
[INFO] [stderr] 125 | fn standard_deviation(vec :&Vec<f32>) -> f32{
[INFO] [stderr]     |                            ^^^^^^^^^ help: change this to: `&[f32]`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `num_lines` is used as a loop counter. Consider using `for (num_lines, item) in my_buffer.lines().enumerate()` or similar iterators
[INFO] [stderr]   --> src/bin/fasten_quality_filter.rs:52:17
[INFO] [stderr]    |
[INFO] [stderr] 52 |     for line in my_buffer.lines() {
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: this if statement can be collapsed
[INFO] [stderr]    --> src/bin/fasten_clean.rs:107:17
[INFO] [stderr]     |
[INFO] [stderr] 107 | /                 if lines_per_read==4 {
[INFO] [stderr] 108 | |                     if seq1_trimmed.len() >= min_length && avg_quality(&qual1_trimmed) >= min_avg_qual {
[INFO] [stderr] 109 | |                         println!("{}\n{}\n+\n{}",
[INFO] [stderr] 110 | |                              id1,seq1_trimmed,qual1_trimmed,
[INFO] [stderr] 111 | |                              );
[INFO] [stderr] 112 | |                     }
[INFO] [stderr] 113 | |                 }
[INFO] [stderr]     | |_________________^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::collapsible_if)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_if
[INFO] [stderr] help: try
[INFO] [stderr]     |
[INFO] [stderr] 107 |                 if lines_per_read==4 && seq1_trimmed.len() >= min_length && avg_quality(&qual1_trimmed) >= min_avg_qual {
[INFO] [stderr] 108 |     println!("{}\n{}\n+\n{}",
[INFO] [stderr] 109 |          id1,seq1_trimmed,qual1_trimmed,
[INFO] [stderr] 110 |          );
[INFO] [stderr] 111 | }
[INFO] [stderr]     |
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_clean.rs:152:5
[INFO] [stderr]     |
[INFO] [stderr] 152 |     return avg;
[INFO] [stderr]     |     ^^^^^^^^^^^ help: remove `return` as shown: `avg`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_clean.rs:190:5
[INFO] [stderr]     |
[INFO] [stderr] 190 |     return(new_seq,new_qual);
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `(new_seq,new_qual)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: `if _ { .. } else { .. }` is an expression
[INFO] [stderr]   --> src/bin/fasten_clean.rs:29:5
[INFO] [stderr]    |
[INFO] [stderr] 29 | /     let mut min_length :usize = 0;
[INFO] [stderr] 30 | |     if matches.opt_present("min-length") {
[INFO] [stderr] 31 | |         min_length = matches.opt_str("min-length")
[INFO] [stderr] 32 | |             .expect("ERROR: could not read the minimum length parameter")
[INFO] [stderr] 33 | |             .parse()
[INFO] [stderr] 34 | |             .expect("ERROR: min-length is not an integer");
[INFO] [stderr] 35 | |     }
[INFO] [stderr]    | |_____^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::useless_let_if_seq)] on by default
[INFO] [stderr]    = note: you might not need `mut` at all
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_let_if_seq
[INFO] [stderr] help: it is more idiomatic to write
[INFO] [stderr]    |
[INFO] [stderr] 29 |     let <mut> min_length = if matches.opt_present("min-length") { matches.opt_str("min-length")
[INFO] [stderr] 30 |             .expect("ERROR: could not read the minimum length parameter")
[INFO] [stderr] 31 |             .parse()
[INFO] [stderr] 32 |             .expect("ERROR: min-length is not an integer") } else { 0 };
[INFO] [stderr]    |
[INFO] [stderr] 
[INFO] [stderr] warning: `if _ { .. } else { .. }` is an expression
[INFO] [stderr]   --> src/bin/fasten_clean.rs:37:5
[INFO] [stderr]    |
[INFO] [stderr] 37 | /     let mut min_avg_qual :f32 = 0.0;
[INFO] [stderr] 38 | |     if matches.opt_present("min-avg-quality") {
[INFO] [stderr] 39 | |         min_avg_qual = matches.opt_str("min-avg-quality")
[INFO] [stderr] 40 | |             .expect("ERROR: could not read the minimum average quality parameter")
[INFO] [stderr] 41 | |             .parse()
[INFO] [stderr] 42 | |             .expect("ERROR: min-avg-qual is not an integer");
[INFO] [stderr] 43 | |     }
[INFO] [stderr]    | |_____^
[INFO] [stderr]    |
[INFO] [stderr]    = note: you might not need `mut` at all
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_let_if_seq
[INFO] [stderr] help: it is more idiomatic to write
[INFO] [stderr]    |
[INFO] [stderr] 37 |     let <mut> min_avg_qual = if matches.opt_present("min-avg-quality") { matches.opt_str("min-avg-quality")
[INFO] [stderr] 38 |             .expect("ERROR: could not read the minimum average quality parameter")
[INFO] [stderr] 39 |             .parse()
[INFO] [stderr] 40 |             .expect("ERROR: min-avg-qual is not an integer") } else { 0.0 };
[INFO] [stderr]    |
[INFO] [stderr] 
[INFO] [stderr] warning: `if _ { .. } else { .. }` is an expression
[INFO] [stderr]   --> src/bin/fasten_clean.rs:45:5
[INFO] [stderr]    |
[INFO] [stderr] 45 | /     let mut min_trim_qual :u8 = 0;
[INFO] [stderr] 46 | |     if matches.opt_present("min-trim-quality") {
[INFO] [stderr] 47 | |         min_trim_qual = matches.opt_str("min-trim-quality")
[INFO] [stderr] 48 | |             .expect("ERROR: could not read the minimum trim quality parameter")
[INFO] [stderr] 49 | |             .parse()
[INFO] [stderr] 50 | |             .expect("ERROR: min-trim-qual is not an integer");
[INFO] [stderr] 51 | |     }
[INFO] [stderr]    | |_____^
[INFO] [stderr]    |
[INFO] [stderr]    = note: you might not need `mut` at all
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_let_if_seq
[INFO] [stderr] help: it is more idiomatic to write
[INFO] [stderr]    |
[INFO] [stderr] 45 |     let <mut> min_trim_qual = if matches.opt_present("min-trim-quality") { matches.opt_str("min-trim-quality")
[INFO] [stderr] 46 |             .expect("ERROR: could not read the minimum trim quality parameter")
[INFO] [stderr] 47 |             .parse()
[INFO] [stderr] 48 |             .expect("ERROR: min-trim-qual is not an integer") } else { 0 };
[INFO] [stderr]    |
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/bin/fasten_clean.rs:146:22
[INFO] [stderr]     |
[INFO] [stderr] 146 | fn avg_quality(qual: &String) -> f32 {
[INFO] [stderr]     |                      ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to u32 may become silently lossy if types change
[INFO] [stderr]    --> src/bin/fasten_clean.rs:149:18
[INFO] [stderr]     |
[INFO] [stderr] 149 |         total += qual_char as u8 as u32;
[INFO] [stderr]     |                  ^^^^^^^^^^^^^^^^^^^^^^ help: try: `u32::from(qual_char as u8)`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::cast_lossless)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/bin/fasten_clean.rs:156:14
[INFO] [stderr]     |
[INFO] [stderr] 156 | fn trim(seq: &String, qual: &String, min_qual: u8) -> (String,String) {
[INFO] [stderr]     |              ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/bin/fasten_clean.rs:156:29
[INFO] [stderr]     |
[INFO] [stderr] 156 | fn trim(seq: &String, qual: &String, min_qual: u8) -> (String,String) {
[INFO] [stderr]     |                             ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: `if _ { .. } else { .. }` is an expression
[INFO] [stderr]    --> src/bin/fasten_clean.rs:181:5
[INFO] [stderr]     |
[INFO] [stderr] 181 | /     let new_qual:String;
[INFO] [stderr] 182 | |     
[INFO] [stderr] 183 | |     if trim5 >= trim3 {
[INFO] [stderr] 184 | |         new_seq = String::new();
[INFO] [stderr] ...   |
[INFO] [stderr] 188 | |         new_qual = qual[trim5..trim3].to_string();
[INFO] [stderr] 189 | |     }
[INFO] [stderr]     | |_____^ help: it is more idiomatic to write: `let new_qual = if trim5 >= trim3 { ..; String::new() } else { ..; qual[trim5..trim3].to_string() };`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_let_if_seq
[INFO] [stderr] 
[INFO] [stderr] warning: this if statement can be collapsed
[INFO] [stderr]    --> src/bin/fasten_clean.rs:107:17
[INFO] [stderr]     |
[INFO] [stderr] 107 | /                 if lines_per_read==4 {
[INFO] [stderr] 108 | |                     if seq1_trimmed.len() >= min_length && avg_quality(&qual1_trimmed) >= min_avg_qual {
[INFO] [stderr] 109 | |                         println!("{}\n{}\n+\n{}",
[INFO] [stderr] 110 | |                              id1,seq1_trimmed,qual1_trimmed,
[INFO] [stderr] 111 | |                              );
[INFO] [stderr] 112 | |                     }
[INFO] [stderr] 113 | |                 }
[INFO] [stderr]     | |_________________^
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::collapsible_if)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_if
[INFO] [stderr] help: try
[INFO] [stderr]     |
[INFO] [stderr] 107 |                 if lines_per_read==4 && seq1_trimmed.len() >= min_length && avg_quality(&qual1_trimmed) >= min_avg_qual {
[INFO] [stderr] 108 |     println!("{}\n{}\n+\n{}",
[INFO] [stderr] 109 |          id1,seq1_trimmed,qual1_trimmed,
[INFO] [stderr] 110 |          );
[INFO] [stderr] 111 | }
[INFO] [stderr]     |
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_clean.rs:152:5
[INFO] [stderr]     |
[INFO] [stderr] 152 |     return avg;
[INFO] [stderr]     |     ^^^^^^^^^^^ help: remove `return` as shown: `avg`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_clean.rs:190:5
[INFO] [stderr]     |
[INFO] [stderr] 190 |     return(new_seq,new_qual);
[INFO] [stderr]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^ help: remove `return` as shown: `(new_seq,new_qual)`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: `if _ { .. } else { .. }` is an expression
[INFO] [stderr]   --> src/bin/fasten_clean.rs:29:5
[INFO] [stderr]    |
[INFO] [stderr] 29 | /     let mut min_length :usize = 0;
[INFO] [stderr] 30 | |     if matches.opt_present("min-length") {
[INFO] [stderr] 31 | |         min_length = matches.opt_str("min-length")
[INFO] [stderr] 32 | |             .expect("ERROR: could not read the minimum length parameter")
[INFO] [stderr] 33 | |             .parse()
[INFO] [stderr] 34 | |             .expect("ERROR: min-length is not an integer");
[INFO] [stderr] 35 | |     }
[INFO] [stderr]    | |_____^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::useless_let_if_seq)] on by default
[INFO] [stderr]    = note: you might not need `mut` at all
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_let_if_seq
[INFO] [stderr] help: it is more idiomatic to write
[INFO] [stderr]    |
[INFO] [stderr] 29 |     let <mut> min_length = if matches.opt_present("min-length") { matches.opt_str("min-length")
[INFO] [stderr] 30 |             .expect("ERROR: could not read the minimum length parameter")
[INFO] [stderr] 31 |             .parse()
[INFO] [stderr] 32 |             .expect("ERROR: min-length is not an integer") } else { 0 };
[INFO] [stderr]    |
[INFO] [stderr] 
[INFO] [stderr] warning: `if _ { .. } else { .. }` is an expression
[INFO] [stderr]   --> src/bin/fasten_clean.rs:37:5
[INFO] [stderr]    |
[INFO] [stderr] 37 | /     let mut min_avg_qual :f32 = 0.0;
[INFO] [stderr] 38 | |     if matches.opt_present("min-avg-quality") {
[INFO] [stderr] 39 | |         min_avg_qual = matches.opt_str("min-avg-quality")
[INFO] [stderr] 40 | |             .expect("ERROR: could not read the minimum average quality parameter")
[INFO] [stderr] 41 | |             .parse()
[INFO] [stderr] 42 | |             .expect("ERROR: min-avg-qual is not an integer");
[INFO] [stderr] 43 | |     }
[INFO] [stderr]    | |_____^
[INFO] [stderr]    |
[INFO] [stderr]    = note: you might not need `mut` at all
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_let_if_seq
[INFO] [stderr] help: it is more idiomatic to write
[INFO] [stderr]    |
[INFO] [stderr] 37 |     let <mut> min_avg_qual = if matches.opt_present("min-avg-quality") { matches.opt_str("min-avg-quality")
[INFO] [stderr] 38 |             .expect("ERROR: could not read the minimum average quality parameter")
[INFO] [stderr] 39 |             .parse()
[INFO] [stderr] 40 |             .expect("ERROR: min-avg-qual is not an integer") } else { 0.0 };
[INFO] [stderr]    |
[INFO] [stderr] 
[INFO] [stderr] warning: `if _ { .. } else { .. }` is an expression
[INFO] [stderr]   --> src/bin/fasten_clean.rs:45:5
[INFO] [stderr]    |
[INFO] [stderr] 45 | /     let mut min_trim_qual :u8 = 0;
[INFO] [stderr] 46 | |     if matches.opt_present("min-trim-quality") {
[INFO] [stderr] 47 | |         min_trim_qual = matches.opt_str("min-trim-quality")
[INFO] [stderr] 48 | |             .expect("ERROR: could not read the minimum trim quality parameter")
[INFO] [stderr] 49 | |             .parse()
[INFO] [stderr] 50 | |             .expect("ERROR: min-trim-qual is not an integer");
[INFO] [stderr] 51 | |     }
[INFO] [stderr]    | |_____^
[INFO] [stderr]    |
[INFO] [stderr]    = note: you might not need `mut` at all
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_let_if_seq
[INFO] [stderr] help: it is more idiomatic to write
[INFO] [stderr]    |
[INFO] [stderr] 45 |     let <mut> min_trim_qual = if matches.opt_present("min-trim-quality") { matches.opt_str("min-trim-quality")
[INFO] [stderr] 46 |             .expect("ERROR: could not read the minimum trim quality parameter")
[INFO] [stderr] 47 |             .parse()
[INFO] [stderr] 48 |             .expect("ERROR: min-trim-qual is not an integer") } else { 0 };
[INFO] [stderr]    |
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/bin/fasten_clean.rs:146:22
[INFO] [stderr]     |
[INFO] [stderr] 146 | fn avg_quality(qual: &String) -> f32 {
[INFO] [stderr]     |                      ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: casting u8 to u32 may become silently lossy if types change
[INFO] [stderr]    --> src/bin/fasten_clean.rs:149:18
[INFO] [stderr]     |
[INFO] [stderr] 149 |         total += qual_char as u8 as u32;
[INFO] [stderr]     |                  ^^^^^^^^^^^^^^^^^^^^^^ help: try: `u32::from(qual_char as u8)`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::cast_lossless)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_lossless
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/bin/fasten_clean.rs:156:14
[INFO] [stderr]     |
[INFO] [stderr] 156 | fn trim(seq: &String, qual: &String, min_qual: u8) -> (String,String) {
[INFO] [stderr]     |              ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/bin/fasten_clean.rs:156:29
[INFO] [stderr]     |
[INFO] [stderr] 156 | fn trim(seq: &String, qual: &String, min_qual: u8) -> (String,String) {
[INFO] [stderr]     |                             ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr] warning: `if _ { .. } else { .. }` is an expression
[INFO] [stderr]    --> src/bin/fasten_clean.rs:181:5
[INFO] [stderr]     |
[INFO] [stderr] 181 | /     let new_qual:String;
[INFO] [stderr] 182 | |     
[INFO] [stderr] 183 | |     if trim5 >= trim3 {
[INFO] [stderr] 184 | |         new_seq = String::new();
[INFO] [stderr] ...   |
[INFO] [stderr] 188 | |         new_qual = qual[trim5..trim3].to_string();
[INFO] [stderr] 189 | |     }
[INFO] [stderr]     | |_____^ help: it is more idiomatic to write: `let new_qual = if trim5 >= trim3 { ..; String::new() } else { ..; qual[trim5..trim3].to_string() };`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#useless_let_if_seq
[INFO] [stderr] 
[INFO] [stderr] warning: using `write!()` with a format string that ends in a single newline, consider using `writeln!()` instead
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:65:13
[INFO] [stderr]    |
[INFO] [stderr] 65 |             write!(file1,"{}\n",seq.to_string()).unwrap();
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::write_with_newline)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#write_with_newline
[INFO] [stderr] 
[INFO] [stderr] warning: using `write!()` with a format string that ends in a single newline, consider using `writeln!()` instead
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:67:13
[INFO] [stderr]    |
[INFO] [stderr] 67 |             write!(file2,"{}\n",seq.to_string()).unwrap();
[INFO] [stderr]    |             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#write_with_newline
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `line_counter` is used as a loop counter. Consider using `for (line_counter, item) in my_buffer.lines().enumerate()` or similar iterators
[INFO] [stderr]   --> src/bin/fasten_sample.rs:54:17
[INFO] [stderr]    |
[INFO] [stderr] 54 |     for line in my_buffer.lines() {
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_pe.rs:131:5
[INFO] [stderr]     |
[INFO] [stderr] 131 |     return 1;
[INFO] [stderr]     |     ^^^^^^^^^ help: remove `return` as shown: `1`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_pe.rs:166:5
[INFO] [stderr]     |
[INFO] [stderr] 166 |     return 1;
[INFO] [stderr]     |     ^^^^^^^^^ help: remove `return` as shown: `1`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]   --> src/bin/fasten_pe.rs:93:35
[INFO] [stderr]    |
[INFO] [stderr] 93 | fn is_paired_end_slash12(id1_ref: &Vec<String>, id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]    |                                   ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] help: change this to
[INFO] [stderr]    |
[INFO] [stderr] 93 | fn is_paired_end_slash12(id1_ref: &[String], id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]    |                                   ^^^^^^^^^
[INFO] [stderr] help: change `id1_ref.clone()` to
[INFO] [stderr]    |
[INFO] [stderr] 96 |     let id1_vec = id1_ref.to_owned();
[INFO] [stderr]    |                   ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]   --> src/bin/fasten_pe.rs:93:58
[INFO] [stderr]    |
[INFO] [stderr] 93 | fn is_paired_end_slash12(id1_ref: &Vec<String>, id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]    |                                                          ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] help: change this to
[INFO] [stderr]    |
[INFO] [stderr] 93 | fn is_paired_end_slash12(id1_ref: &Vec<String>, id2_ref: &[String]) -> u8 {
[INFO] [stderr]    |                                                          ^^^^^^^^^
[INFO] [stderr] help: change `id2_ref.clone()` to
[INFO] [stderr]    |
[INFO] [stderr] 97 |     let id2_vec = id2_ref.to_owned();
[INFO] [stderr]    |                   ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/bin/fasten_pe.rs:135:33
[INFO] [stderr]     |
[INFO] [stderr] 135 | fn is_paired_end_miseq(id1_ref: &Vec<String>, id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]     |                                 ^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] help: change this to
[INFO] [stderr]     |
[INFO] [stderr] 135 | fn is_paired_end_miseq(id1_ref: &[String], id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]     |                                 ^^^^^^^^^
[INFO] [stderr] help: change `id1_ref.clone()` to
[INFO] [stderr]     |
[INFO] [stderr] 137 |     let id1_vec = id1_ref.to_owned();
[INFO] [stderr]     |                   ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&Vec<_>` instead of `&[_]` involves one more reference and cannot be used with non-Vec-based slices.
[INFO] [stderr]    --> src/bin/fasten_pe.rs:135:56
[INFO] [stderr]     |
[INFO] [stderr] 135 | fn is_paired_end_miseq(id1_ref: &Vec<String>, id2_ref: &Vec<String>) -> u8 {
[INFO] [stderr]     |                                                        ^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] help: change this to
[INFO] [stderr]     |
[INFO] [stderr] 135 | fn is_paired_end_miseq(id1_ref: &Vec<String>, id2_ref: &[String]) -> u8 {
[INFO] [stderr]     |                                                        ^^^^^^^^^
[INFO] [stderr] help: change `id2_ref.clone()` to
[INFO] [stderr]     |
[INFO] [stderr] 138 |     let id2_vec = id2_ref.to_owned();
[INFO] [stderr]     |                   ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: single-character string constant used as pattern
[INFO] [stderr]    --> src/bin/fasten_pe.rs:149:33
[INFO] [stderr]     |
[INFO] [stderr] 149 |         let id1_tmp = id1.split(":").nth(6);
[INFO] [stderr]     |                                 ^^^ help: try using a char instead: `':'`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::single_char_pattern)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern
[INFO] [stderr] 
[INFO] [stderr] warning: single-character string constant used as pattern
[INFO] [stderr]    --> src/bin/fasten_pe.rs:150:33
[INFO] [stderr]     |
[INFO] [stderr] 150 |         let id2_tmp = id2.split(":").nth(6);
[INFO] [stderr]     |                                 ^^^ help: try using a char instead: `':'`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern
[INFO] [stderr] 
[INFO] [stderr] warning: single-character string constant used as pattern
[INFO] [stderr]    --> src/bin/fasten_pe.rs:156:54
[INFO] [stderr]     |
[INFO] [stderr] 156 |         let id1_read_number = id1_tmp.unwrap().split(" ").nth(1);
[INFO] [stderr]     |                                                      ^^^ help: try using a char instead: `' '`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern
[INFO] [stderr] 
[INFO] [stderr] warning: single-character string constant used as pattern
[INFO] [stderr]    --> src/bin/fasten_pe.rs:157:54
[INFO] [stderr]     |
[INFO] [stderr] 157 |         let id2_read_number = id2_tmp.unwrap().split(" ").nth(1);
[INFO] [stderr]     |                                                      ^^^ help: try using a char instead: `' '`
[INFO] [stderr]     |
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#single_char_pattern
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]   --> src/bin/fasten_randomize.rs:35:48
[INFO] [stderr]    |
[INFO] [stderr] 35 | fn print_reads_from_stdin(lines_per_read :u32) -> () {
[INFO] [stderr]    |                                                ^^^^^ help: remove the `-> ()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::unused_unit)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: long literal lacking separators
[INFO] [stderr]   --> src/bin/fasten_randomize.rs:37:52
[INFO] [stderr]    |
[INFO] [stderr] 37 |     let mut seqs :Vec<String> = Vec::with_capacity(100000);
[INFO] [stderr]    |                                                    ^^^^^^ help: consider: `100_000`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::unreadable_literal)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unreadable_literal
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `num_lines` is used as a loop counter. Consider using `for (num_lines, item) in my_buffer.lines().enumerate()` or similar iterators
[INFO] [stderr]   --> src/bin/fasten_trim.rs:60:17
[INFO] [stderr]    |
[INFO] [stderr] 60 |     for line in my_buffer.lines() {
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:39:42
[INFO] [stderr]    |
[INFO] [stderr] 39 | fn deshuffle(matches: &getopts::Matches) -> () {
[INFO] [stderr]    |                                          ^^^^^ help: remove the `-> ()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::unused_unit)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded unit return type
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:74:40
[INFO] [stderr]    |
[INFO] [stderr] 74 | fn shuffle(matches: &getopts::Matches) -> () {
[INFO] [stderr]    |                                        ^^^^^ help: remove the `-> ()`
[INFO] [stderr]    |
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unused_unit
[INFO] [stderr] 
[INFO] [stderr] warning: unneeded return statement
[INFO] [stderr]    --> src/bin/fasten_shuffle.rs:117:5
[INFO] [stderr]     |
[INFO] [stderr] 117 |     return seqs;
[INFO] [stderr]     |     ^^^^^^^^^^^^ help: remove `return` as shown: `seqs`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::needless_return)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_return
[INFO] [stderr] 
[INFO] [stderr] warning: the variable `read_counter` is used as a loop counter. Consider using `for (read_counter, item) in fastq_reader.enumerate()` or similar iterators
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:61:16
[INFO] [stderr]    |
[INFO] [stderr] 61 |     for seq in fastq_reader {
[INFO] [stderr]    |                ^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::explicit_counter_loop)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#explicit_counter_loop
[INFO] [stderr] 
[INFO] [stderr] warning: length comparison to zero
[INFO] [stderr]   --> src/bin/fasten_shuffle.rs:97:8
[INFO] [stderr]    |
[INFO] [stderr] 97 |     if seqs2.len() == 0 {
[INFO] [stderr]    |        ^^^^^^^^^^^^^^^^ help: using `is_empty` is clearer and more explicit: `seqs2.is_empty()`
[INFO] [stderr]    |
[INFO] [stderr]    = note: #[warn(clippy::len_zero)] on by default
[INFO] [stderr]    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#len_zero
[INFO] [stderr] 
[INFO] [stderr] warning: writing `&String` instead of `&str` involves a new object where a slice will do.
[INFO] [stderr]    --> src/bin/fasten_shuffle.rs:111:24
[INFO] [stderr]     |
[INFO] [stderr] 111 | fn read_seqs(filename: &String) -> Vec<Seq> {
[INFO] [stderr]     |                        ^^^^^^^ help: change this to: `&str`
[INFO] [stderr]     |
[INFO] [stderr]     = note: #[warn(clippy::ptr_arg)] on by default
[INFO] [stderr]     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
[INFO] [stderr] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 23.13s
[INFO] running `"docker" "inspect" "e23ecc15233c93006e1ae1d79dec0c7cee54e571b7ada1bf0ced9f5f4f559723"`
[INFO] running `"docker" "rm" "-f" "e23ecc15233c93006e1ae1d79dec0c7cee54e571b7ada1bf0ced9f5f4f559723"`
[INFO] [stdout] e23ecc15233c93006e1ae1d79dec0c7cee54e571b7ada1bf0ced9f5f4f559723