Added standard pre-commit script that runs formatting, clippy and tests.

Cargo.toml

@@ -12,27 +12,38 @@ readme = "README.md"
 categories = ["science"]
 keywords = ["bioinformatics", "fastq"]
 
+[lib]
+name = "fqgrep_lib"
+path = "src/lib/mod.rs"
+
+[[bin]]
+name = "fqgrep"
+path = "src/main.rs"
+
 
 [profile.release]
 lto = true
 
 [dependencies]
+ansi_term = "0.12.1"
 anyhow = "1.0.44"
+bitvec = "1.0.1"
 bstr = "0.2.17"
 csv = "1.1.6"
 env_logger = "0.9.0"
 flate2 = {version = "1.0.22", default-features = false, features = ["zlib-ng-compat"]}
 flume = "0.10.9"
 gzp = "0.9.1"
-itertools = "0.10.1"
+isatty = "0.1.9"
+itertools = "0.10.3"
 lazy_static = "1.4.0"
 log = "0.4.14"
 mimalloc = {version = "0.1.26", default-features = false}
 num_cpus = "1.13.0"
 parking_lot = "0.11.2"
 proglog = {version = "0.3.0", features = ["pretty_counts"]}
 rayon = "1.5.1"
-regex = "1.5.4"
+regex = "1.6.0"
 seq_io = "0.3.1"
 serde = {version = "1.0.130", features = ["derive"]}
 structopt = "0.3.23"

precommit.sh

@@ -0,0 +1,55 @@
+#!/usr/bin/env bash
+
+###############################################################################
+# Script that should be run pre-commit after making any changes.
+###############################################################################
+
+set -e
+
+failures=""
+
+function banner() {
+    echo
+    echo "================================================================================"
+    echo $*
+    echo "================================================================================"
+    echo
+}
+
+#####################################################################
+# Takes two parameters, a "name" and a "command". 
+# Runs the command and prints out whether it succeeded or failed, and
+# also tracks a list of failed steps in $failures.
+#####################################################################
+function run() {
+    local name=$1
+    local cmd=$2
+
+    banner "Running $name"
+    set +e
+    $cmd
+    exit_code=$?
+    set -e
+
+    if [[ $exit_code == 0 ]]; then
+        echo Passed $name 
+    else
+        echo Failed $name
+        if [ -z "$failures" ]; then
+            failures="$name"
+        else
+            failures="$failures, $name"
+        fi
+    fi
+}
+
+run "cargo fmt"    "cargo fmt --all"
+run "cargo clippy" "cargo clippy --all-features --locked -- -D warnings"
+run "cargo test"   "cargo test --locked --quiet"
+
+if [ -z "$failures" ]; then
+    banner "Precommit Passed"
+else
+    banner "Precommit Failed with failures in: $failures"
+    exit 1
+fi

rust-toolchain.toml

@@ -0,0 +1,3 @@
+[toolchain]
+channel = "1.64.0"
+components = ["rustfmt", "clippy"]

src/lib/color.rs

@@ -0,0 +1,32 @@
+use ansi_term::Color;
+
+/// Color for matching bases in a FASTQ
+pub const COLOR_BASES: Color = Color::Red;
+/// Color for matching base qualities in a FASTQ
+pub const COLOR_QUALS: Color = Color::Fixed(22);
+/// Color for a matching read name (head) of a FASTQ
+pub const COLOR_HEAD: Color = Color::Fixed(30);
+/// Color for all non-matching text in a FASTQ
+pub const COLOR_BACKGROUND: Color = Color::Fixed(240);
+
+/// Colors the text with the given color
+pub fn color(text: &[u8], colour: &Color) -> Vec<u8> {
+    let mut colored: Vec<u8> = Vec::with_capacity(text.len());
+    colour.paint(text).write_to(&mut colored).unwrap();
+    colored
+}
+
+/// Color for the read name (head) of a FASTQ
+pub fn color_head(text: &[u8]) -> Vec<u8> {
+    color(text, &COLOR_HEAD)
+}
+
+/// Color for the base qualities of a FASTQ
+pub fn color_quals(text: &[u8]) -> Vec<u8> {
+    color(text, &COLOR_QUALS)
+}
+
+/// Color for non-matching bases, quals, and other text
+pub fn color_background(text: &[u8]) -> Vec<u8> {
+    color(text, &COLOR_BACKGROUND)
+}