Add in --version (#10)

* making moves to streamline arg parsing and add in --version

* refactored getopts

* m

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name    = "fasten"
-version = "0.4.3"
+version = "0.4.4"
 authors = ["Lee Katz <[email protected]>"]
 #license-file  = "LICENSE"
 license       = "MIT"

src/bin/fasten_clean.rs

@@ -39,12 +39,12 @@ extern crate threadpool;
 use std::fs::File;
 use std::io::BufReader;
 use std::io::BufRead;
-use std::env;
 
 use threadpool::ThreadPool;
 use std::sync::mpsc::channel;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 //use fasten::logmsg;
 
 #[test]
@@ -128,7 +128,6 @@ D>C1'02C+=I@IEFHC7&-E5',I?E*33E/@3#68B%\"!B-/2%(G=*@D052IA!('7-*$+A6>.$89,-CG71=
 }
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
 
     // invisible option but maybe we can expose it:
@@ -140,12 +139,7 @@ fn main(){
     opts.optopt("","min-avg-quality","Minimum average quality for each read","FLOAT");
     opts.optopt("","min-trim-quality","Trim the edges of each read until a nucleotide of at least X quality is found","INT");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-
-    if matches.opt_present("h") {
-        println!("{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Trims and filters reads", opts);
 
     let mut min_length :usize = 0;
     if matches.opt_present("min-length") {

src/bin/fasten_combine.rs

@@ -36,10 +36,10 @@ use std::io::stdin;
 //use std::io::BufRead;
 use std::collections::HashMap;
 
-use std::env;
 use std::f32;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fastq::{Parser, Record};
 use fasten::logmsg;
 
@@ -51,7 +51,6 @@ const TEN: f32 = 10.0;
 const READ_SEPARATOR :char = '~';
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
 
     // make a string of characters like !"#...GHI to represent all quals
@@ -72,15 +71,9 @@ fn main(){
       format!("Minimum quality character (default: {})", default_phred_min_char).as_str(),
       "CHAR");
 
-    let matches = opts.parse(&args[1..]).expect("Parsing parameters");
+    let description:String = format!("Collapse identical reads into single reads, recalculating quality values. If paired end, then each set of reads must be identical to be collapsed. Warning: due to multiple reads collapsing into one, read identifiers will be reconstituted. NOTE: range of quality scores is {}", qual_range_string);
+    let matches = fasten_base_options_matches(&description, opts);
 
-    if matches.opt_present("h") {
-        println!("Collapse identical reads into single reads, recalculating quality values. If paired end, then each set of reads must be identical to be collapsed. Warning: due to multiple reads collapsing into one, read identifiers will be reconstituted.");
-        println!("{}",opts.usage(&opts.short_usage(&args[0])));
-        println!("NOTE: range of quality scores is {}", qual_range_string);
-        std::process::exit(0);
-    }
-
     let max_qual_char:char = matches.opt_default("max-qual-char", &default_phred_max_char.to_string())
                      .unwrap_or(String::from(default_phred_max_char))
                      .parse()

src/bin/fasten_convert.rs

@@ -38,13 +38,12 @@ extern crate bam;
 use bam::RecordReader;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fasten::logmsg;
 
 use std::io::stdin;
 use fastq::{Parser, Record};
 
-use std::env;
-
 use std::sync::mpsc::channel;
 
 /// Struct that can handle paired end reads
@@ -123,16 +122,12 @@ fn test_fastq_to () {
 */
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
-    opts.optopt("i", "in-format",  "The input format for stdin",  "FORMAT");
-    opts.optopt("o", "out-format", "The output format for stdin", "FORMAT");
+    opts.optopt("i", "in-format",  "The input format for stdin. FORMAT can be: fastq, fasta, sam.",  "FORMAT");
+    opts.optopt("o", "out-format", "The output format for stdin. See --in-format for FORMAT options.", "FORMAT");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-    if matches.opt_present("help") {
-        println!("{}  FORMAT can be: fastq, fasta, sam\n", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let description:String = format!("Converts between sequence formats.");
+    let matches = fasten_base_options_matches(&description, opts);
 
     let paired_end = matches.opt_present("paired-end");
 

src/bin/fasten_kmer.rs

@@ -27,11 +27,11 @@ extern crate getopts;
 
 use std::io::BufReader;
 use std::io::BufRead;
-use std::env;
 use std::io::stdin;
 use std::io::Stdin;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fasten::logmsg;
 
 use std::collections::HashMap;
@@ -85,20 +85,15 @@ fn test_kmer_counting_4mers () {
 }
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
 
     // script-specific options
     let default_k:usize = 21;
     opts.optopt("k","kmer-length",&format!("The size of the kmer (default: {})",default_k),"INT");
     opts.optflag("r","revcomp", "Count kmers on the reverse complement strand too");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-
-    if matches.opt_present("help") {
-        println!("Counts kmers.\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Counts kmers.", opts);
+
     if matches.opt_present("paired-end") {
         logmsg("WARNING: --paired-end is not utilized in this script");
     }

src/bin/fasten_metrics.rs

@@ -33,9 +33,8 @@ use std::io::BufReader;
 use std::io::BufRead;
 use std::f32;
 
-use std::env;
-
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fasten::logmsg;
 
 #[test]
@@ -53,19 +52,14 @@ fn test_average_quality () {
 }
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
 
     // script-specific options
     opts.optflag("","each-read","Print the metrics for each read. This creates very large output");
     opts.optopt("","distribution","Print the distribution for each metric. Must supply either 'normal' or 'nonparametric'","STRING");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
+    let matches = fasten_base_options_matches("Gives read metrics on a read set.", opts);
 
-    if matches.opt_present("help") {
-        println!("Gives read metrics on a read set.\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
     if matches.opt_present("paired-end") {
         logmsg("WARNING: --paired-end is not utilized in this script");
     }

src/bin/fasten_mutate.rs

@@ -29,26 +29,21 @@ extern crate rand;
 use std::fs::File;
 use std::io::BufReader;
 use std::io::BufRead;
-use std::env;
 
 use rand::distributions::{IndependentSample, Range};
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fasten::logmsg;
 
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
     // Options specific to this script
     opts.optopt("s", "snps", "Number of SNPs (point mutations) to include per read.", "INT");
     opts.optflag("m", "mark", "lowercase all reads but uppercase the SNPs (not yet implemented)");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-    if matches.opt_present("help") {
-        println!("Mutates reads. There is no mutation model; only randomness.\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Mutates reads. There is no mutation model; only randomness.", opts);
 
     if matches.opt_present("paired-end") {
         logmsg("WARNING: --paired-end is not utilized in this script");

src/bin/fasten_pe.rs

@@ -28,27 +28,19 @@ extern crate fasten;
 extern crate regex;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fasten::logmsg;
 use regex::Regex;
 
 use std::fs::File;
 use std::io::BufReader;
 use std::io::BufRead;
-use std::env;
 
 fn main() {
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
-    //opts.optopt("c","check-first","How many deflines to check to make sure the input is paired-end","INT");
     opts.optflag("","print-reads","Print each read. Useful for Unix pipes.");
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
+    let matches = fasten_base_options_matches("Determine paired-end-ness in an interleaved file. Exit code of 0 indicates PE. Exit code > 0 indicates SE.", opts);
 
-    if matches.opt_present("help") {
-        println!("Determine paired-end-ness in an interleaved file. Exit code of 0 indicates PE. Exit code > 0 indicates SE.\n{}", 
-                 opts.usage(&opts.short_usage(&args[0]))
-                );
-        std::process::exit(0);
-    }
     if matches.opt_present("paired-end") {
         logmsg("WARNING: --paired-end was supplied but this script is supposed to determine whether the input is paired-end.");
     }

src/bin/fasten_progress.rs

@@ -48,23 +48,18 @@ extern crate fasten;
 use std::fs::File;
 use std::io::BufReader;
 use std::io::BufRead;
-use std::env;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
     // Options specific to this script
     opts.optopt("","id","Progress identifier. Default: unnamed","STRING");
     opts.optopt("","update-every","Update progress every n reads.","INT");
     opts.optflag("p","print","Print the reads back to stdout");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-    if matches.opt_present("help") {
-        println!("Prints a progress meter for number of fastq entries.\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Prints a progress meter for number of fastq entries", opts);
 
     let print_reads:bool = matches.opt_present("print");
 

src/bin/fasten_quality_filter.rs

@@ -27,24 +27,19 @@ extern crate getopts;
 use std::fs::File;
 use std::io::BufReader;
 use std::io::BufRead;
-use std::env;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fasten::logmsg;
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
 
     // script-specific options
     opts.optopt("m","max-quality","The maximum quality at which a base will be transformed to 'N'","INT");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-
-    if matches.opt_present("help") {
-        println!("Transforms any low-quality base to 'N'\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Transforms any low-quality base to 'N'.", opts);
+
     if matches.opt_present("paired-end") {
         logmsg("WARNING: --paired-end is not utilized in this script");
     }

src/bin/fasten_randomize.rs

@@ -39,22 +39,16 @@ extern crate rand;
 use std::fs::File;
 use std::io::BufReader;
 use std::io::BufRead;
-use std::env;
 
 use rand::{Rng,thread_rng};
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let opts = fasten_base_options();
-    //script-specific flags
 
-    let matches = opts.parse(&args[1..]).expect("Error: could not parse parameters");
-    if matches.opt_present("help") {
-        println!("Create random reads from stdin.\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Create random reads from stdin.", opts);
 
     let lines_per_read :u32={
         if matches.opt_present("paired-end") {

src/bin/fasten_regex.rs

@@ -37,27 +37,22 @@ extern crate threadpool;
 use std::fs::File;
 use std::io::BufReader;
 use std::io::BufRead;
-use std::env;
 
 use regex::Regex;
 use threadpool::ThreadPool;
 use std::sync::mpsc::channel;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
     // Options specific to this script
     opts.optopt("r","regex","Regular expression (default: '.')","STRING");
     opts.optopt("w","which","Which field to match on? ID, SEQ, QUAL. Default: SEQ","String");
     //opts.optflag("e","exclude","Exclude these reads instead of including them");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-    if matches.opt_present("help") {
-        println!("Filter reads based on a regular expression.\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Filter reads based on a regular expression.", opts);
 
     let (tx, rx):(std::sync::mpsc::Sender<String>,std::sync::mpsc::Receiver<String>) = channel();
 

src/bin/fasten_replace.rs

@@ -32,26 +32,21 @@ extern crate regex;
 use std::fs::File;
 use std::io::BufReader;
 use std::io::BufRead;
-use std::env;
 
 use regex::Regex;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fasten::logmsg;
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
     // Options specific to this script
     opts.optopt("f","find","Regular expression (default: '.')","STRING");
     opts.optopt("r","replace","String to replace each match","STRING");
     opts.optopt("w","which","Which field to match on? ID, SEQ, QUAL. Default: SEQ","STRING");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-    if matches.opt_present("help") {
-        println!("Streaming editor for fastq data using a find/replace.\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Streaming editor for fastq data using a find/replace.", opts);
 
     if matches.opt_present("paired-end") {
         logmsg("WARNING: --paired-end is not utilized in this script");