From fb003330f05a3539cdabddee55bdf9e489944786 Mon Sep 17 00:00:00 2001
From: Garrett Ng <56460265+GarrettNg@users.noreply.github.com>
Date: Mon, 13 Nov 2023 15:56:43 -0500
Subject: [PATCH] Revert unintended commits to main branch

Revert "Implement file like object compatibility for fastq reader"
This reverts commit 9ff35a8a35084c13a1450687dac4d2921991be6b.

Revert "Restructure imports and remove unused code"
This reverts commit 2279ab7bb09d371b2b3335727ae0b0c2f7eb992e.
---
 oxbow/src/fastq.rs  | 48 +++++++++++++++++++++------------------------
 py-oxbow/src/lib.rs | 20 ++++---------------
 2 files changed, 26 insertions(+), 42 deletions(-)

diff --git a/oxbow/src/fastq.rs b/oxbow/src/fastq.rs
index 92520c4..516510d 100644
--- a/oxbow/src/fastq.rs
+++ b/oxbow/src/fastq.rs
@@ -1,35 +1,31 @@
 use arrow::array::{ArrayRef, GenericStringBuilder};
 use arrow::{error::ArrowError, record_batch::RecordBatch};
+// use noodles::core::Region;
 use noodles::fastq;
-use std::{
-    fs::File,
-    io::{self, BufReader, Read, Seek},
-    str,
-    sync::Arc,
-};
+// use noodles::fastq::fai;
+use std::sync::Arc;
 
 use crate::batch_builder::{write_ipc, BatchBuilder};
 
-/// A FASTQ reader.
-pub struct FastqReader<R> {
-    reader: fastq::Reader<BufReader<R>>,
-}
+type BufferedReader = std::io::BufReader<std::fs::File>;
 
-impl FastqReader<BufReader<File>> {
-    /// Creates a Fasta reader from a given file path.
-    pub fn new_from_path(path: &str) -> io::Result<Self> {
-        let reader = File::open(path)
-            .map(BufReader::new)
-            .map(BufReader::new)
-            .map(fastq::Reader::new)?;
-        Ok(Self { reader })
-    }
+/// A FASTQ reader.
+pub struct FastqReader {
+    reader: fastq::Reader<BufferedReader>,
+    // index: fai::Reader<std::io::BufReader<std::fs::File>>,
 }
 
-impl<R: Read + Seek> FastqReader<R> {
+impl FastqReader {
     /// Creates a Fastq Reader.
-    pub fn new(read: R) -> io::Result<Self> {
-        let reader = fastq::Reader::new(BufReader::new(read));
+    pub fn new(path: &str) -> std::io::Result<Self> {
+        // let index_file = std::fs::File::open(format!("{}.fai", path))?;
+        // let index_bufreader = std::io::BufReader::with_capacity(1024 * 1024, index_file);
+        // let index = fai::Reader::new(index_bufreader);
+
+        let file = std::fs::File::open(path)?;
+        let bufreader = std::io::BufReader::with_capacity(1024 * 1024, file);
+        let reader = fastq::reader::Reader::new(bufreader);
+
         Ok(Self { reader })
     }
 
@@ -75,13 +71,13 @@ impl BatchBuilder for FastqBatchBuilder {
 
     fn push(&mut self, record: Self::Record<'_>) {
         self.name
-            .append_value(str::from_utf8(record.name()).unwrap());
+            .append_value(std::str::from_utf8(record.name()).unwrap());
         self.description
-            .append_value(str::from_utf8(record.description()).unwrap());
+            .append_value(std::str::from_utf8(record.description()).unwrap());
         self.sequence
-            .append_value(str::from_utf8(record.sequence()).unwrap());
+            .append_value(std::str::from_utf8(record.sequence()).unwrap());
         self.quality_scores
-            .append_value(str::from_utf8(record.quality_scores()).unwrap());
+            .append_value(std::str::from_utf8(record.quality_scores()).unwrap());
     }
 
     fn finish(mut self) -> Result<RecordBatch, ArrowError> {
diff --git a/py-oxbow/src/lib.rs b/py-oxbow/src/lib.rs
index 18f5446..f000b18 100644
--- a/py-oxbow/src/lib.rs
+++ b/py-oxbow/src/lib.rs
@@ -39,22 +39,10 @@ fn read_fasta(path: &str, region: Option<&str>) -> PyObject {
 }
 
 #[pyfunction]
-fn read_fastq(py: Python, path_or_file_like: PyObject) -> PyObject {
-    if let Ok(string_ref) = path_or_file_like.downcast::<PyString>(py) {
-        // If it's a string, treat it like a path
-        let mut reader = FastqReader::new_from_path(string_ref.to_str().unwrap()).unwrap();
-        let ipc = reader.records_to_ipc().unwrap();
-        Python::with_gil(|py| PyBytes::new(py, &ipc).into())
-    } else {
-        // Otherwise, treat it as file-like
-        let file_like = match PyFileLikeObject::new(path_or_file_like, true, false, true) {
-	    Ok(file_like) => file_like,
-            Err(_) => panic!("Unknown argument for `path_url_or_file_like`. Not a file path string or url, and not a file-like object."),
-	};
-        let mut reader = FastqReader::new(file_like).unwrap();
-        let ipc = reader.records_to_ipc().unwrap();
-        Python::with_gil(|py| PyBytes::new(py, &ipc).into())
-    }
+fn read_fastq(path: &str) -> PyObject {
+    let mut reader = FastqReader::new(path).unwrap();
+    let ipc = reader.records_to_ipc().unwrap();
+    Python::with_gil(|py| PyBytes::new(py, &ipc).into())
 }
 
 #[pyfunction]