diff --git a/Cargo.toml b/Cargo.toml
index bb29c035..b9396c8c 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name    = "fasten"
-version = "0.4.3"
+version = "0.4.4"
 authors = ["Lee Katz <gzu2@cdc.gov>"]
 #license-file  = "LICENSE"
 license       = "MIT"
diff --git a/src/bin/fasten_clean.rs b/src/bin/fasten_clean.rs
index b8686510..6416b128 100644
--- a/src/bin/fasten_clean.rs
+++ b/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") {
diff --git a/src/bin/fasten_combine.rs b/src/bin/fasten_combine.rs
index 69f97be2..46c6db57 100644
--- a/src/bin/fasten_combine.rs
+++ b/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()
diff --git a/src/bin/fasten_convert.rs b/src/bin/fasten_convert.rs
index 447d4037..5049589d 100644
--- a/src/bin/fasten_convert.rs
+++ b/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");
 
diff --git a/src/bin/fasten_kmer.rs b/src/bin/fasten_kmer.rs
index a4eef0d0..891fdb5c 100644
--- a/src/bin/fasten_kmer.rs
+++ b/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;
@@ -85,7 +85,6 @@ fn test_kmer_counting_4mers () {
 }
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
 
     // script-specific options
@@ -93,12 +92,8 @@ fn main(){
     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");
     }
diff --git a/src/bin/fasten_metrics.rs b/src/bin/fasten_metrics.rs
index f5c61091..2482ef43 100644
--- a/src/bin/fasten_metrics.rs
+++ b/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");
     }
diff --git a/src/bin/fasten_mutate.rs b/src/bin/fasten_mutate.rs
index a7856ae8..2fcf43d7 100644
--- a/src/bin/fasten_mutate.rs
+++ b/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");
diff --git a/src/bin/fasten_pe.rs b/src/bin/fasten_pe.rs
index c44a45bf..d997a991 100644
--- a/src/bin/fasten_pe.rs
+++ b/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.");
     }
diff --git a/src/bin/fasten_progress.rs b/src/bin/fasten_progress.rs
index b2ea0725..2d83e9e4 100644
--- a/src/bin/fasten_progress.rs
+++ b/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");
 
diff --git a/src/bin/fasten_quality_filter.rs b/src/bin/fasten_quality_filter.rs
index 32877070..beb27728 100644
--- a/src/bin/fasten_quality_filter.rs
+++ b/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");
     }
diff --git a/src/bin/fasten_randomize.rs b/src/bin/fasten_randomize.rs
index 81e0c2bd..2c014870 100644
--- a/src/bin/fasten_randomize.rs
+++ b/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") {
diff --git a/src/bin/fasten_regex.rs b/src/bin/fasten_regex.rs
index 199ca5c8..3170323b 100644
--- a/src/bin/fasten_regex.rs
+++ b/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();
 
diff --git a/src/bin/fasten_replace.rs b/src/bin/fasten_replace.rs
index 00c6495c..04790129 100644
--- a/src/bin/fasten_replace.rs
+++ b/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");
diff --git a/src/bin/fasten_sample.rs b/src/bin/fasten_sample.rs
index 36097b28..f0eb592f 100644
--- a/src/bin/fasten_sample.rs
+++ b/src/bin/fasten_sample.rs
@@ -29,25 +29,18 @@ use std::fs::File;
 use std::io::BufReader;
 use std::io::BufRead;
 
-use std::env;
-
 use rand::thread_rng;
 use rand::Rng;
 
 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();
 
     opts.optopt("f","frequency","Frequency of sequences to print, 0 to 1. Default: 1","FLOAT");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-
-    if matches.opt_present("help") {
-        println!("Ursula: downsample your reads\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Downsample your reads", opts);
 
     let frequency :f32 = {
         if matches.opt_present("frequency") {
diff --git a/src/bin/fasten_shuffle.rs b/src/bin/fasten_shuffle.rs
index 13952f33..a54e8350 100644
--- a/src/bin/fasten_shuffle.rs
+++ b/src/bin/fasten_shuffle.rs
@@ -52,26 +52,21 @@ use std::io::Write;
 use std::io::BufReader;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fasten::io::fastq;
 use fasten::io::seq::Cleanable;
 use fasten::io::seq::Seq;
 use fasten::logmsg;
 
-use std::env;
-
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
     //script-specific flags
     opts.optflag("d","deshuffle","Deshuffle reads from stdin");
     opts.optopt("1","","Forward reads. If deshuffling, reads are written to this file.","1.fastq");
     opts.optopt("2","","Forward reads. If deshuffling, reads are written to this file.","2.fastq");
 
-    let matches = opts.parse(&args[1..]).expect("Error: could not parse parameters");
-    if matches.opt_present("help") {
-        println!("Interleaves reads from either stdin or file parameters.\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Interleaves reads from either stdin or file parameters", opts);
+    
     if matches.opt_present("paired-end") {
         logmsg("WARNING: --paired-end was supplied but it is assumed for this script anyway");
     }
diff --git a/src/bin/fasten_sort.rs b/src/bin/fasten_sort.rs
index 2bbd350c..a4e7d4a2 100644
--- a/src/bin/fasten_sort.rs
+++ b/src/bin/fasten_sort.rs
@@ -55,9 +55,9 @@ extern crate threadpool;
 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;
 
 #[test]
@@ -137,17 +137,12 @@ struct Seq {
 }
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
     // Options specific to this script
     opts.optopt("s","sort-by","Sort by either SEQ, GC, or ID. If GC, then the entries are sorted by GC percentage. SEQ and ID are alphabetically sorted.","STRING");
     opts.optflag("r","reverse","Reverse sort");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-    if matches.opt_present("help") {
-        println!("Sort reads.\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Sort reads. This can be useful for many things including checksums and reducing gzip file sizes. Remember to use --paired-end if applicable.", opts);
 
     let my_file = File::open("/dev/stdin").expect("Could not open file");
     let my_buffer=BufReader::new(my_file);
@@ -235,6 +230,7 @@ fn sort_entries (unsorted:Vec<Seq>, which_field:&str, reverse_sort:bool) -> Vec<
     let mut sorted = unsorted.clone();
 
     // Actual sort
+    // TODO sort by length?
     match which_field{
         "ID" => {
             sorted.sort_by(|a, b| {
diff --git a/src/bin/fasten_straighten.rs b/src/bin/fasten_straighten.rs
index 328f5748..842613d0 100644
--- a/src/bin/fasten_straighten.rs
+++ b/src/bin/fasten_straighten.rs
@@ -24,12 +24,11 @@ use std::fs::File;
 use std::io::BufReader;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fasten::io::fastq;
 use fasten::io::seq::Cleanable;
 use fasten::logmsg;
 
-use std::env;
-
 #[test]
 /// Test to see whether we read the challenge dataset correctly
 fn challenge_dataset () {
@@ -56,13 +55,9 @@ fn challenge_dataset () {
 
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let opts = fasten_base_options();
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-    if matches.opt_present("help") {
-        println!("Convert a fastq file to a standard 4-lines-per-entry format\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Convert a fastq file to a standard 4-lines-per-entry format", opts);
+    
     if matches.opt_present("paired-end") {
         logmsg("WARNING: --paired-end is not utilized in this script");
     }
diff --git a/src/bin/fasten_trim.rs b/src/bin/fasten_trim.rs
index 6f5ff03c..4d7dfc10 100644
--- a/src/bin/fasten_trim.rs
+++ b/src/bin/fasten_trim.rs
@@ -39,32 +39,26 @@ extern crate threadpool;
 
 use std::fs::File;
 use std::io::BufReader;
-use std::env;
 use std::cmp::min;
 
 use threadpool::ThreadPool;
 use std::sync::mpsc::channel;
 
 use fasten::fasten_base_options;
+use fasten::fasten_base_options_matches;
 use fasten::logmsg;
 use fasten::io::fastq;
 use fasten::io::seq::Cleanable;
 use fasten::io::seq::Seq;
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
 
     // script-specific options
     opts.optopt("f","first-base","The first base to keep (default: 0)","INT");
     opts.optopt("l","last-base","The last base to keep. If negative, counts from the right. (default: 0)","INT");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-
-    if matches.opt_present("help") {
-        println!("Blunt-end trims using 0-based coordinates\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Blunt-end trims using 0-based coordinates", opts);
 
     let (tx, rx):(std::sync::mpsc::Sender<String>,std::sync::mpsc::Receiver<String>) = channel();
 
diff --git a/src/bin/fasten_validate.rs b/src/bin/fasten_validate.rs
index 94a61b81..ebc012e3 100644
--- a/src/bin/fasten_validate.rs
+++ b/src/bin/fasten_validate.rs
@@ -41,7 +41,6 @@
 //!             --paired-end    The reads are interleaved paired-end
 //!             --print-reads   Print the reads as they are being validated (useful
 //!                             for unix pipes)
-//!         -v, --verbose       
 //! ```
 
 extern crate getopts;
@@ -50,27 +49,21 @@ 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;
 
 fn main(){
-    let args: Vec<String> = env::args().collect();
     let mut opts = fasten_base_options();
     // Options specific to this script
     opts.optopt("","min-length","Minimum read length allowed","INT");
     opts.optopt("","min-quality","Minimum quality allowed","FLOAT");
     opts.optflag("","paired-end","The reads are interleaved paired-end");
     opts.optflag("","print-reads","Print the reads as they are being validated (useful for unix pipes)");
-    opts.optflag("v","verbose","");
 
-    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
-    if matches.opt_present("help") {
-        println!("Validates your reads and makes you feel good about yourself!\n{}", opts.usage(&opts.short_usage(&args[0])));
-        std::process::exit(0);
-    }
+    let matches = fasten_base_options_matches("Validates your reads and makes you feel good about yourself!", opts);
 
     let my_file = File::open("/dev/stdin").expect("Could not open file");
     let my_buffer=BufReader::new(my_file);
diff --git a/src/lib.rs b/src/lib.rs
index a0956134..67d8d139 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -67,10 +67,13 @@ use std::env;
 use std::path::Path;
 
 use getopts::Options;
+use getopts::Matches;
 
 /// input/output methods
 pub mod io;
 
+const VERSION: &'static str = env!("CARGO_PKG_VERSION");
+
 /// Have some strings that can be printed which could be
 /// used to propagate errors between piped scripts.
 
@@ -112,11 +115,44 @@ pub fn fasten_base_options() -> Options{
     opts.optflag("h", "help", "Print this help menu.");
     opts.optopt("n","numcpus","Number of CPUs (default: 1)","INT");
     opts.optflag("p","paired-end","The input reads are interleaved paired-end");
-    opts.optflag("v","verbose","Print more status messages");
+    opts.optflag("","verbose","Print more status messages");
+    opts.optflag("","version","Print the version of Fasten and exit");
 
     return opts;
 }
 
+/// a function that processes the options on the command line
+/// The brief is a str that describes the program without using the program
+/// name, e.g., "counts kmers" for fasten_kmer.
+/// This function also takes care of --version.
+/// If --help is invoked, then the program name, the brief, and the usage()
+/// are all printed to stdout and then the program exits with 0.
+// TODO if possible add in default somehow for numcpus
+pub fn fasten_base_options_matches(brief:&str, opts:Options) -> Matches{
+    let args: Vec<String> = env::args().collect();
+    let matches = opts.parse(&args[1..]).expect("ERROR: could not parse parameters");
+
+    if matches.opt_present("version") {
+        println!("Fasten v{}", &VERSION);
+        std::process::exit(0);
+    }
+    if matches.opt_present("h") {
+        let prog_name = Path::new(&args[0])
+            .file_stem().unwrap()
+            .to_str().unwrap();
+        println!("{}: {}\n\n{}", 
+                 &prog_name,
+                 &brief,
+                 &opts.usage(
+                     &opts.short_usage(&prog_name)
+                 ),
+        );
+        std::process::exit(0);
+    }
+
+    return matches;
+}
+
 /// Print a formatted message to stderr 
 pub fn logmsg<S: AsRef<str>>(stringlike: S) {
     let args: Vec<_> = env::args().collect();