feat: Update rust-bio (#202)

* Update to rust_bio 0.39

* update rust-bio

Author: FelixMoelder

Cargo.toml

@@ -10,7 +10,7 @@ readme = "README.md"
 
 [dependencies]
 approx = "0.4"
-bio = "0.32"
+bio = "0.39"
 clap = { version = "2.31", features = ["yaml", "color", "suggestions"]}
 indicatif = "0.11"
 itertools = "0.9"

src/bam/anonymize_reads.rs

@@ -9,7 +9,7 @@ use std::ops::Range;
 use std::path::Path;
 use uuid::Uuid;
 
-pub fn anonymize_reads<P: AsRef<Path>>(
+pub fn anonymize_reads<P: AsRef<Path> + std::fmt::Debug>(
     bam: P,
     input_ref: P,
     output_bam: P,

src/bam/plot/plot_bam.rs

@@ -9,7 +9,7 @@ use std::io::Write;
 use std::path::Path;
 use tera::{Context, Tera};
 
-pub(crate) fn plot_bam<P: AsRef<Path>>(
+pub(crate) fn plot_bam<P: AsRef<Path> + std::fmt::Debug>(
     bam_paths: &[P],
     fasta_path: P,
     region: &Region,

src/bcf/report/table_report/alignment_reader.rs

@@ -142,7 +142,7 @@ fn make_alignment(record: &bam::Record) -> Alignment {
     }
 }
 
-pub fn make_nucleobases<P: AsRef<Path>>(
+pub fn make_nucleobases<P: AsRef<Path> + std::fmt::Debug>(
     fasta_path: P,
     region: &Region,
     snippets: Vec<Alignment>,

src/bcf/report/table_report/create_report_table.rs

@@ -502,7 +502,7 @@ pub(crate) fn read_tag_entries(
     Ok(())
 }
 
-pub(crate) fn create_report_data<P: AsRef<Path>>(
+pub(crate) fn create_report_data<P: AsRef<Path> + std::fmt::Debug>(
     fasta_path: P,
     variant: Option<Variant>,
     bam_path: P,

src/bcf/report/table_report/fasta_reader.rs

@@ -7,7 +7,7 @@ use serde::Serialize;
 use std::collections::HashMap;
 use std::path::Path;
 
-pub fn read_fasta<P: AsRef<Path>>(
+pub fn read_fasta<P: AsRef<Path> + std::fmt::Debug>(
     path: P,
     region: &Region,
     compensate_0_basing: bool,

src/bcf/report/table_report/static_reader.rs

@@ -142,7 +142,7 @@ fn calc_rows(
     (reads_wr, matches_wr)
 }
 
-pub fn get_static_reads<P: AsRef<Path>>(
+pub fn get_static_reads<P: AsRef<Path> + std::fmt::Debug>(
     path: P,
     fasta_path: P,
     region: &Region,

src/fastq/collapse_reads_to_fragments/mod.rs

@@ -94,7 +94,7 @@ use std::path::Path;
 /// The type of the readers (writers) depends on the file ending.
 /// If the input file names end with '.gz' a gzipped reader (writer) is used.
 #[allow(clippy::too_many_arguments)]
-pub fn call_consensus_reads_from_paths<P: AsRef<Path>>(
+pub fn call_consensus_reads_from_paths<P: AsRef<Path> + std::fmt::Debug>(
     fq1: P,
     fq2: P,
     fq1_out: P,
@@ -121,7 +121,9 @@ pub fn call_consensus_reads_from_paths<P: AsRef<Path>>(
                 fq2_out.as_ref().display()
             );
 
-            fn reader<P: AsRef<Path>>(path: P) -> Result<fastq::Reader<Box<dyn std::io::Read>>> {
+            fn reader<P: AsRef<Path>>(
+                path: P,
+            ) -> Result<fastq::Reader<BufReader<Box<dyn std::io::Read>>>> {
                 let r: Box<dyn Read> = if path.as_ref().ends_with(".gz") {
                     Box::new(
                         fs::File::open(&path)

src/fastq/collapse_reads_to_fragments/pipeline.rs

@@ -111,7 +111,7 @@ pub struct NonOverlappingConsensus {
     likelihood: LogProb,
 }
 
-pub trait CallConsensusReads<'a, R: io::Read + 'a, W: io::Write + 'a> {
+pub trait CallConsensusReads<'a, R: io::Read + io::BufRead + 'a, W: io::Write + 'a> {
     /// Cluster reads from fastq readers according to their sequence
     /// and UMI, then compute a consensus sequence.
     ///
@@ -312,7 +312,7 @@ pub struct CallNonOverlappingConsensusRead<'a, R: io::Read, W: io::Write> {
     verbose_read_names: bool,
 }
 
-impl<'a, R: io::Read, W: io::Write> CallConsensusReads<'a, R, W>
+impl<'a, R: io::Read + io::BufRead, W: io::Write> CallConsensusReads<'a, R, W>
     for CallNonOverlappingConsensusRead<'a, R, W>
 {
     fn write_records(
@@ -480,7 +480,7 @@ impl<'a, R: io::Read, W: io::Write> CallOverlappingConsensusRead<'a, R, W> {
     }
 }
 
-impl<'a, R: io::Read, W: io::Write> CallConsensusReads<'a, R, W>
+impl<'a, R: io::Read + io::BufRead, W: io::Write> CallConsensusReads<'a, R, W>
     for CallOverlappingConsensusRead<'a, R, W>
 {
     fn write_records(