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[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/bluenote-1577/rs-liftover
[INFO] finished tweaking git repo https://github.com/bluenote-1577/rs-liftover
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[INFO] [stdout] warning: unused import: `Header`
[INFO] [stdout]  --> src/parse_files.rs:6:32
[INFO] [stdout]   |
[INFO] [stdout] 6 | use rust_htslib::bam::header::{Header, HeaderRecord};
[INFO] [stdout]   |                                ^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserialize` and `Serialize`
[INFO] [stdout]  --> src/parse_files.rs:9:13
[INFO] [stdout]   |
[INFO] [stdout] 9 | use serde::{Deserialize, Serialize};
[INFO] [stdout]   |             ^^^^^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs`
[INFO] [stdout]   --> src/parse_files.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::fs;
[INFO] [stdout]    |     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::prelude::*`
[INFO] [stdout]   --> src/parse_files.rs:14:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::prelude::*;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::sync::Mutex`
[INFO] [stdout]   --> src/parse_files.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use std::sync::Mutex;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `App` and `SubCommand`
[INFO] [stdout]  --> src/main.rs:3:12
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |            ^^^                             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Header`
[INFO] [stdout]  --> src/parse_files.rs:6:32
[INFO] [stdout]   |
[INFO] [stdout] 6 | use rust_htslib::bam::header::{Header, HeaderRecord};
[INFO] [stdout]   |                                ^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Deserialize` and `Serialize`
[INFO] [stdout]  --> src/parse_files.rs:9:13
[INFO] [stdout]   |
[INFO] [stdout] 9 | use serde::{Deserialize, Serialize};
[INFO] [stdout]   |             ^^^^^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs`
[INFO] [stdout]   --> src/parse_files.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::fs;
[INFO] [stdout]    |     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::prelude::*`
[INFO] [stdout]   --> src/parse_files.rs:14:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::prelude::*;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::sync::Mutex`
[INFO] [stdout]   --> src/parse_files.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use std::sync::Mutex;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `App` and `SubCommand`
[INFO] [stdout]  --> src/main.rs:3:12
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |            ^^^                             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `clap::App`: Replaced with `Command`
[INFO] [stdout]  --> src/main.rs:3:12
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |            ^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `clap::SubCommand`: Replaced with `Command::new` unless you intended the `Subcommand` trait
[INFO] [stdout]  --> src/main.rs:3:44
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |                                            ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated unit variant `clap::AppSettings::ArgRequiredElseHelp`: Replaced with `Command::arg_required_else_help` and `Command::is_arg_required_else_help_set`
[INFO] [stdout]  --> src/main.rs:7:31
[INFO] [stdout]   |
[INFO] [stdout] 7 |         .setting(AppSettings::ArgRequiredElseHelp)
[INFO] [stdout]   |                               ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `clap::App`: Replaced with `Command`
[INFO] [stdout]  --> src/main.rs:3:12
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |            ^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `clap::SubCommand`: Replaced with `Command::new` unless you intended the `Subcommand` trait
[INFO] [stdout]  --> src/main.rs:3:44
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |                                            ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated unit variant `clap::AppSettings::ArgRequiredElseHelp`: Replaced with `Command::arg_required_else_help` and `Command::is_arg_required_else_help_set`
[INFO] [stdout]  --> src/main.rs:7:31
[INFO] [stdout]   |
[INFO] [stdout] 7 |         .setting(AppSettings::ArgRequiredElseHelp)
[INFO] [stdout]   |                               ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `header` found for struct `rust_htslib::bam::Reader` in the current scope
[INFO] [stdout]    --> src/parse_files.rs:184:53
[INFO] [stdout]     |
[INFO] [stdout] 184 |     let mut header = bam::Header::from_template(bam.header());
[INFO] [stdout]     |                                                     ^^^^^^ private field, not a method
[INFO] [stdout]     |
[INFO] [stdout]    ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:168:8
[INFO] [stdout]     |
[INFO] [stdout] 168 |     fn header(&self) -> &HeaderView;
[INFO] [stdout]     |        ------ the method is available for `rust_htslib::bam::Reader` here
[INFO] [stdout]     |
[INFO] [stdout]     = help: items from traits can only be used if the trait is in scope
[INFO] [stdout] help: there is a method `read` with a similar name, but with different arguments
[INFO] [stdout]    --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:116:5
[INFO] [stdout]     |
[INFO] [stdout] 116 |     fn read(&mut self, record: &mut record::Record) -> Option<Result<()>>;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] help: trait `Read` which provides `header` is implemented but not in scope; perhaps you want to import it
[INFO] [stdout]     |
[INFO] [stdout]   1 + use rust_htslib::bam::Read;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `header` found for struct `rust_htslib::bam::Reader` in the current scope
[INFO] [stdout]    --> src/parse_files.rs:184:53
[INFO] [stdout]     |
[INFO] [stdout] 184 |     let mut header = bam::Header::from_template(bam.header());
[INFO] [stdout]     |                                                     ^^^^^^ private field, not a method
[INFO] [stdout]     |
[INFO] [stdout]    ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:168:8
[INFO] [stdout]     |
[INFO] [stdout] 168 |     fn header(&self) -> &HeaderView;
[INFO] [stdout]     |        ------ the method is available for `rust_htslib::bam::Reader` here
[INFO] [stdout]     |
[INFO] [stdout]     = help: items from traits can only be used if the trait is in scope
[INFO] [stdout] help: there is a method `read` with a similar name, but with different arguments
[INFO] [stdout]    --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:116:5
[INFO] [stdout]     |
[INFO] [stdout] 116 |     fn read(&mut self, record: &mut record::Record) -> Option<Result<()>>;
[INFO] [stdout]     |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] help: trait `Read` which provides `header` is implemented but not in scope; perhaps you want to import it
[INFO] [stdout]     |
[INFO] [stdout]   1 + use rust_htslib::bam::Read;
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `records` found for struct `rust_htslib::bam::Reader` in the current scope
[INFO] [stdout]    --> src/parse_files.rs:198:20
[INFO] [stdout]     |
[INFO] [stdout] 198 |     for rec in bam.records() {
[INFO] [stdout]     |                    ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:126:8
[INFO] [stdout]     |
[INFO] [stdout] 126 |     fn records(&mut self) -> Records<'_, Self>;
[INFO] [stdout]     |        ------- the method is available for `rust_htslib::bam::Reader` here
[INFO] [stdout]     |
[INFO] [stdout]     = help: items from traits can only be used if the trait is in scope
[INFO] [stdout] help: trait `Read` which provides `records` is implemented but not in scope; perhaps you want to import it
[INFO] [stdout]     |
[INFO] [stdout]   1 + use rust_htslib::bam::Read;
[INFO] [stdout]     |
[INFO] [stdout] help: there is a method `rc_records` with a similar name
[INFO] [stdout]     |
[INFO] [stdout] 198 |     for rec in bam.rc_records() {
[INFO] [stdout]     |                     +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0282]: type annotations needed
[INFO] [stdout]    --> src/parse_files.rs:199:22
[INFO] [stdout]     |
[INFO] [stdout] 199 |         let record = rec.unwrap();
[INFO] [stdout]     |                      ^^^ cannot infer type
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0599]: no method named `records` found for struct `rust_htslib::bam::Reader` in the current scope
[INFO] [stdout]    --> src/parse_files.rs:198:20
[INFO] [stdout]     |
[INFO] [stdout] 198 |     for rec in bam.records() {
[INFO] [stdout]     |                    ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.39.5/src/bam/mod.rs:126:8
[INFO] [stdout]     |
[INFO] [stdout] 126 |     fn records(&mut self) -> Records<'_, Self>;
[INFO] [stdout]     |        ------- the method is available for `rust_htslib::bam::Reader` here
[INFO] [stdout]     |
[INFO] [stdout]     = help: items from traits can only be used if the trait is in scope
[INFO] [stdout] help: trait `Read` which provides `records` is implemented but not in scope; perhaps you want to import it
[INFO] [stdout]     |
[INFO] [stdout]   1 + use rust_htslib::bam::Read;
[INFO] [stdout]     |
[INFO] [stdout] help: there is a method `rc_records` with a similar name
[INFO] [stdout]     |
[INFO] [stdout] 198 |     for rec in bam.rc_records() {
[INFO] [stdout]     |                     +++
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0282]: type annotations needed
[INFO] [stdout]    --> src/parse_files.rs:199:22
[INFO] [stdout]     |
[INFO] [stdout] 199 |         let record = rec.unwrap();
[INFO] [stdout]     |                      ^^^ cannot infer type
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/parse_files.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/parse_files.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0282, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0282`.
[INFO] [stdout] 
[INFO] [stdout] Some errors have detailed explanations: E0282, E0599.
[INFO] [stdout] 
[INFO] [stdout] For more information about an error, try `rustc --explain E0282`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `rs-liftover` (bin "rs-liftover") due to 3 previous errors; 10 warnings emitted
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] [stderr] error: could not compile `rs-liftover` (bin "rs-liftover" test) due to 3 previous errors; 10 warnings emitted
[INFO] running `Command { std: "docker" "inspect" "b73ec97bdee632cd38fad454d4a17af16ecb1f039b89f1b0a40c48f3e28db34b", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "b73ec97bdee632cd38fad454d4a17af16ecb1f039b89f1b0a40c48f3e28db34b", kill_on_drop: false }`
[INFO] [stdout] b73ec97bdee632cd38fad454d4a17af16ecb1f039b89f1b0a40c48f3e28db34b
