From aa2b61206674a90dcf1d028ade936ec3a1bd16c4 Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Fri, 18 Aug 2023 10:53:39 +0200
Subject: [PATCH] moving average and base-quality stubs

---
 src/bin/commands/trimmer.rs |  8 ++++
 src/bin/main.rs             |  4 +-
 src/lib/base_quality.rs     | 78 +++++++++++++++++++++++++++++++++++++
 src/lib/mod.rs              |  1 +
 src/lib/moving_average.rs   | 40 +++++++++++++++++++
 5 files changed, 129 insertions(+), 2 deletions(-)
 create mode 100644 src/lib/base_quality.rs
 create mode 100644 src/lib/moving_average.rs

diff --git a/src/bin/commands/trimmer.rs b/src/bin/commands/trimmer.rs
index 9a65e94..893c74f 100644
--- a/src/bin/commands/trimmer.rs
+++ b/src/bin/commands/trimmer.rs
@@ -19,6 +19,14 @@ pub(crate) struct TrimmerOpts {
     #[clap(long, short = 't', default_value = "5")]
     threads: usize,
 
+    /// Minimum base-quality to keep a base when trimming tails.
+    #[clap(long, short = 'q', default_value = "20")]
+    trim_tail_quality: u8,
+
+    /// Window size for moving average when trimming tails.
+    #[clap(long, short = 'w', default_value = "20")]
+    trim_tail_window: u8,
+
     /// Level of compression to use to compress outputs.
     #[clap(long, short = 'c', default_value = "5")]
     compression_level: usize,
diff --git a/src/bin/main.rs b/src/bin/main.rs
index 1e78df1..c42202b 100644
--- a/src/bin/main.rs
+++ b/src/bin/main.rs
@@ -5,7 +5,7 @@ pub mod commands;
 use anyhow::Result;
 use clap::Parser;
 use commands::command::Command;
-use commands::{demux::Demux, trimmer::Trimmer};
+use commands::{demux::Demux, trimmer::TrimmerOpts};
 use enum_dispatch::enum_dispatch;
 use env_logger::Env;
 
@@ -23,7 +23,7 @@ struct Args {
 #[command(version)]
 enum Subcommand {
     Demux(Demux),
-    Trimmer(Trimmer),
+    Trimmer(TrimmerOpts),
 }
 
 fn main() -> Result<()> {
diff --git a/src/lib/base_quality.rs b/src/lib/base_quality.rs
new file mode 100644
index 0000000..2739422
--- /dev/null
+++ b/src/lib/base_quality.rs
@@ -0,0 +1,78 @@
+use std::ops::Range;
+
+pub(crate) fn find_oscillating_quals(bqs: &[u8]) -> Range<usize> {
+    return 0..0;
+}
+
+pub(crate) enum Tail {
+    Left,
+    Right,
+    Both,
+}
+
+/// A simple moving average calculator.
+/// Only requires that T is convertable to f64.
+/// Uses space of window * size_of(T) bytes.
+struct MovingAverage<T> {
+    window: usize,
+    values: Vec<T>,
+    sum: f64,
+    idx: usize,
+}
+
+impl<T: Copy + Default + std::convert::Into<f64>> MovingAverage<T> {
+    /// create a new moving average calculator with a window of `window` values.
+    fn new(window: usize) -> Self {
+        Self { window, values: vec![T::default(); window], sum: 0.0, idx: 0 }
+    }
+
+    /// push a new value into the moving average calculator and get the new mean.
+    fn push(&mut self, value: T) -> f64 {
+        let old_value = self.values[self.idx];
+        self.values[self.idx] = value;
+        self.sum = self.sum + value.into() - old_value.into();
+        self.idx = (self.idx + 1) % self.window;
+        self.mean()
+    }
+
+    /// get the current mean.
+    #[inline]
+    fn mean(&self) -> f64 {
+        self.sum / (self.window as f64)
+    }
+}
+
+pub(crate) fn find_low_quality_bases(
+    bqs: &[u8],
+    min_quality: u8,
+    window: u8,
+    tail: Tail,
+) -> Range<usize> {
+    if matches!(tail, Tail::Left | Tail::Both) {
+        let mut i = 0;
+        while i < bqs.len() && bqs[i] < min_quality {
+            i += 1;
+        }
+        return 0..i;
+    }
+    if matches!(tail, Tail::Right | Tail::Both) {
+        let mut i = bqs.len() - 1;
+        while i > 0 && bqs[i] < min_quality {
+            i -= 1;
+        }
+        return i..bqs.len();
+    }
+    0..0
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_find_oscillating_quals() {
+        let bqs = b"!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJ";
+        let range = find_oscillating_quals(bqs);
+        assert_eq!(range, 0..0);
+    }
+}
diff --git a/src/lib/mod.rs b/src/lib/mod.rs
index 022a1e7..3b650df 100644
--- a/src/lib/mod.rs
+++ b/src/lib/mod.rs
@@ -1,4 +1,5 @@
 pub mod barcode_matching;
+pub mod base_quality;
 pub mod pair_overlap;
 pub mod samples;
 
diff --git a/src/lib/moving_average.rs b/src/lib/moving_average.rs
new file mode 100644
index 0000000..63f0f1a
--- /dev/null
+++ b/src/lib/moving_average.rs
@@ -0,0 +1,40 @@
+/// A simple moving average calculator.
+/// Only requires that T is convertable to f64.
+/// Uses space of window * size_of(T) bytes.
+struct MovingAverage<T> {
+    window: usize,
+    values: Vec<T>,
+    sum: f64,
+    idx: usize,
+}
+
+impl<T: Copy + Default + std::convert::Into<f64>> MovingAverage<T> {
+    /// create a new moving average calculator with a window of `window` values.
+    fn new(window: usize) -> Self {
+        Self { window, values: vec![T::default(); window], sum: 0.0, idx: 0 }
+    }
+
+    /// push a new value into the moving average calculator and get the new mean.
+    fn push(&mut self, value: T) -> f64 {
+        let old_value = self.values[self.idx];
+        self.values[self.idx] = value;
+        self.sum = self.sum + value.into() - old_value.into();
+        self.idx = (self.idx + 1) % self.window;
+        self.mean()
+    }
+
+    /// get the current mean.
+    #[inline]
+    fn mean(&self) -> f64 {
+        self.sum / (self.window as f64)
+    }
+}
+
+// write some tests for the calculator
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_moving_average() {}
+}