Cargo fmt

src/bam/call_consensus_reads/mod.rs

@@ -4,7 +4,7 @@ mod pipeline;
 use log::info;
 use pipeline::CallConsensusRead;
 use rust_htslib::bam;
-use rust_htslib::bam::{Header, Read, Format};
+use rust_htslib::bam::{Format, Header, Read};
 use std::error::Error;
 
 pub fn call_consensus_reads_from_paths(
@@ -16,7 +16,11 @@ pub fn call_consensus_reads_from_paths(
     info!("Reading input files:\n    {}", bam_in);
     info!("Writing output to:\n    {}", bam_out);
     let bam_reader = bam::Reader::from_path(bam_in)?;
-    let bam_writer = bam::Writer::from_path(bam_out, &Header::from_template(bam_reader.header()), Format::BAM)?;
+    let bam_writer = bam::Writer::from_path(
+        bam_out,
+        &Header::from_template(bam_reader.header()),
+        Format::BAM,
+    )?;
     CallConsensusRead::new(bam_reader, bam_writer, seq_dist, verbose_read_names)
         .call_consensus_reads()
 }

src/bcf/annotate_dgidb.rs

@@ -2,7 +2,7 @@ use itertools::Itertools;
 use regex::Regex;
 use reqwest;
 use rust_htslib::bcf;
-use rust_htslib::bcf::{Read, Format};
+use rust_htslib::bcf::{Format, Read};
 use serde::{Deserialize, Serialize};
 use std::collections::{HashMap, HashSet};
 use std::error::Error;
@@ -102,13 +102,11 @@ fn extract_genes<'a>(
 ) -> Result<Option<impl Iterator<Item = String> + 'a>, Box<dyn Error>> {
     let annotation = rec.info("ANN".as_bytes()).string()?;
     match annotation {
-        Some(transcripts) => Ok(Some(transcripts.into_iter().map(
-            |transcript| {
-                str::from_utf8(transcript.split(|c| *c == b'|').nth(3).unwrap())
-                    .unwrap()
-                    .to_owned()
-            },
-        ))),
+        Some(transcripts) => Ok(Some(transcripts.into_iter().map(|transcript| {
+            str::from_utf8(transcript.split(|c| *c == b'|').nth(3).unwrap())
+                .unwrap()
+                .to_owned()
+        }))),
         None => Ok(None),
     }
 }

src/bcf/baf.rs

@@ -9,7 +9,7 @@ use itertools::repeat_n;
 use itertools::Itertools;
 use rust_htslib::bcf;
 use rust_htslib::bcf::record::Numeric;
-use rust_htslib::bcf::{Read, Format};
+use rust_htslib::bcf::{Format, Read};
 use std::error::Error;
 use std::f32;
 

src/bcf/fix_iupac_alleles.rs

@@ -1,35 +1,45 @@
 use std::error::Error;
 
-use itertools::Itertools;
 use bio::alphabets::dna::n_alphabet;
-use rust_htslib::bcf::{self, Read, Format};
+use itertools::Itertools;
+use rust_htslib::bcf::{self, Format, Read};
 
 pub fn fix_iupac_alleles() -> Result<(), Box<dyn Error>> {
     let mut inbcf = bcf::Reader::from_stdin()?;
-    let mut outbcf = bcf::Writer::from_stdout(&bcf::Header::from_template(inbcf.header()), false, Format::BCF)?;
+    let mut outbcf = bcf::Writer::from_stdout(
+        &bcf::Header::from_template(inbcf.header()),
+        false,
+        Format::BCF,
+    )?;
     let valid_alphabet = n_alphabet();
 
     for res in inbcf.records() {
         let mut rec = res?;
 
         let alleles = rec.alleles();
         if !alleles.iter().all(|allele| valid_alphabet.is_word(*allele)) {
-            let fixed = alleles.into_iter().map(|allele| {
-                let fixed = allele.into_iter().map(|base| {
-                    if valid_alphabet.is_word(&[*base]) {
-                        *base
-                    } else {
-                        b'N'
-                    }
-                }).collect_vec();
-                fixed
-            }).collect_vec();
+            let fixed = alleles
+                .into_iter()
+                .map(|allele| {
+                    let fixed = allele
+                        .into_iter()
+                        .map(|base| {
+                            if valid_alphabet.is_word(&[*base]) {
+                                *base
+                            } else {
+                                b'N'
+                            }
+                        })
+                        .collect_vec();
+                    fixed
+                })
+                .collect_vec();
 
             rec.set_alleles(&fixed.iter().map(|allele| allele.as_slice()).collect_vec())?;
         }
-        
+
         outbcf.write(&rec)?;
     }
 
     Ok(())
-}
+}

src/bcf/match_variants.rs

@@ -13,7 +13,7 @@ use itertools::Itertools;
 use log::{info, warn};
 use quick_error::quick_error;
 use rust_htslib::bcf;
-use rust_htslib::bcf::{Read, Format};
+use rust_htslib::bcf::{Format, Read};
 use std::collections::{btree_map, BTreeMap, HashMap};
 use std::error::Error;
 use std::str;
@@ -32,7 +32,7 @@ impl VarIndex {
             match reader.read(&mut rec) {
                 Ok(true) => (),
                 Ok(false) => break,
-                Err(e) => return Err(Box::new(e)) 
+                Err(e) => return Err(Box::new(e)),
             };
             if let Some(rid) = rec.rid() {
                 let chrom = reader.header().rid2name(rid)?;
@@ -82,7 +82,7 @@ pub fn match_variants(
         match inbcf.read(&mut rec) {
             Ok(true) => (),
             Ok(false) => break,
-            Err(e) => return Err(Box::new(e)) 
+            Err(e) => return Err(Box::new(e)),
         };
         outbcf.translate(&mut rec);
 

src/bcf/mod.rs

@@ -1,6 +1,6 @@
 //! Tools that work on VCF and BCF files.
 pub mod annotate_dgidb;
 pub mod baf;
+pub mod fix_iupac_alleles;
 pub mod match_variants;
 pub mod to_txt;
-pub mod fix_iupac_alleles;

src/bcf/to_txt.rs

@@ -111,7 +111,7 @@ pub fn to_txt(
         match reader.read(&mut rec) {
             Ok(true) => (),
             Ok(false) => break,
-            Err(e) => return Err(Box::new(e)) 
+            Err(e) => return Err(Box::new(e)),
         };
         let alleles = rec
             .alleles()

tests/lib.rs

@@ -128,9 +128,15 @@ fn vcf_match_same() {
 #[test]
 fn vcf_fix_iupac_alleles() {
     assert!(Command::new("bash")
-            .arg("-c")
-            .arg("target/debug/rbt vcf-fix-iupac-alleles < tests/test-iupac.vcf > tests/iupac-fixed.bcf")
-            .spawn().unwrap().wait().unwrap().success());
+        .arg("-c")
+        .arg(
+            "target/debug/rbt vcf-fix-iupac-alleles < tests/test-iupac.vcf > tests/iupac-fixed.bcf"
+        )
+        .spawn()
+        .unwrap()
+        .wait()
+        .unwrap()
+        .success());
     test_output("tests/iupac-fixed.bcf", "tests/expected/iupac-fixed.bcf");
 }