bump clap version

Author: umieat

Cargo.lock

@@ -7,7 +7,7 @@ edition = "2018"
 [dependencies]
 anyhow = "1.0.53"
 bytecount = "0.6.2"
-clap = "3.0.14"
+clap = "3.1.8"
 itertools = "0.10.3"
 nanoserde = "0.1.29"
 rand = {version = "0.8.4", features = ["getrandom", "small_rng"]}

Cargo.toml

@@ -6,7 +6,7 @@ edition = "2018"
 
 
 [dependencies]
-anyhow = "1.0.34"
-clap = "3.0.0-beta.2"
-itertools = "0.10.0"
+anyhow = "1.0.53"
+clap = "3.1.8"
+itertools = "0.10.3"
 seq_io = "0.3.1"

examples/nuc_profile/Cargo.lock

@@ -1,7 +1,7 @@
 use std::{collections::HashMap, str};
 
 use anyhow::Context;
-use clap::{App, Arg};
+use clap::{Arg, Command};
 use itertools::Itertools;
 use seq_io::{
     fasta::Reader as faReader,
@@ -143,12 +143,12 @@ impl<'a> Fastx<'a> {
 }
 
 fn main() -> anyhow::Result<()> {
-    let matches = App::new("nuc_profile")
+    let matches = Command::new("nuc_profile")
         .version("0.1.0")
         .about("Generate nucleotide profile from FASTA or FASTQ")
         .arg(
             Arg::new("reads")
-                .about("File containing input reads")
+                .help("File containing input reads")
                 .long("reads")
                 .short('R')
                 .takes_value(true)
@@ -157,7 +157,7 @@ fn main() -> anyhow::Result<()> {
         )
         .arg(
             Arg::new("format")
-                .about("Input file format")
+                .help("Input file format")
                 .long("format")
                 .short('F')
                 .takes_value(true)
@@ -166,15 +166,15 @@ fn main() -> anyhow::Result<()> {
         )
         .arg(
             Arg::new("kmer")
-                .about("Kmer size to be used while calculating frequency")
+                .help("Kmer size to be used while calculating frequency")
                 .long("kmer")
                 .takes_value(true)
                 .value_name("INT")
                 .default_value("1"),
         )
         .arg(
             Arg::new("oligo_len")
-                .about("Oligomer length which nucleotide frequency is calculated for")
+                .help("Oligomer length which nucleotide frequency is calculated for")
                 .long("len")
                 .takes_value(true)
                 .value_name("INT")

examples/nuc_profile/Cargo.toml

@@ -7,7 +7,7 @@ use std::{
 
 use anyhow::Context;
 use bytecount::count;
-use clap::{App, Arg};
+use clap::{Arg, Command};
 use itertools::Itertools;
 use nanoserde::DeRon;
 use rand::{prelude::SliceRandom, rngs::SmallRng, Rng, SeedableRng};
@@ -235,7 +235,7 @@ impl<'a> Fastx<'a> {
                             len: record_seq.len(),
                         });
 
-                        update_distmap(&mut ndist, &record_seq, kmer);
+                        update_distmap(&mut ndist, record_seq, kmer);
                     }
                 }
                 normalize_distmap(&mut ndist);
@@ -369,7 +369,7 @@ impl<'a> Fastx<'a> {
                     _ => "+",
                 };
 
-                update_distmap(&mut out_dist, &seq, kmer);
+                update_distmap(&mut out_dist, seq, kmer);
 
                 if let Some(ref mut bed_file) = bed_file {
                     bed_file.write_all(
@@ -560,7 +560,7 @@ fn reverse_complement(input: &[u8]) -> Vec<u8> {
 }
 
 fn main() -> anyhow::Result<()> {
-    let matches = App::new("boquila")
+    let matches = Command::new("boquila")
         .version("0.6.0")
         .about("Generate NGS reads with same nucleotide distribution as input file\nGenerated reads will be written to stdout\nBy default input and output format is FASTQ")
         .arg(Arg::new("src").help("Model file").index(1).required(true))