From 2cf3baa5a412672a86ffed1f541c9f22196d0fe2 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 18 Sep 2024 06:59:42 +1000
Subject: [PATCH] contig: strobealign-aemb: Initial efforts.

---
 src/lib.rs              |  1 +
 src/strobealign_aemb.rs | 67 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 68 insertions(+)
 create mode 100644 src/strobealign_aemb.rs

diff --git a/src/lib.rs b/src/lib.rs
index ac0ee89..bb659a6 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -13,6 +13,7 @@ pub mod mapping_index_maintenance;
 pub mod mapping_parameters;
 pub mod mosdepth_genome_coverage_estimators;
 pub mod shard_bam_reader;
+pub mod strobealign_aemb;
 
 use rust_htslib::bam::record::Record;
 use std::sync::Arc;
diff --git a/src/strobealign_aemb.rs b/src/strobealign_aemb.rs
new file mode 100644
index 0000000..10e18f8
--- /dev/null
+++ b/src/strobealign_aemb.rs
@@ -0,0 +1,67 @@
+use crate::bam_generator::complete_processes;
+use crate::coverage_takers::*;
+use crate::mapping_parameters::MappingParameters;
+use crate::mosdepth_genome_coverage_estimators::*;
+use crate::ReadsMapped;
+
+pub fn strobealign_aemb_coverage<T: CoverageTaker>(
+    mapping_parameters: MappingParameters,
+    _coverage_taker: &mut T,
+    _coverage_estimators: &mut [CoverageEstimator],
+    // print_zero_coverage_contigs: bool,
+    threads: u16,
+) -> Vec<ReadsMapped> {
+    let mut commands = vec![];
+    let mut log_files = vec![];
+
+    for p1 in mapping_parameters {
+        for p2 in p1 {
+            let mapping_result = tempfile::Builder::new()
+                .prefix("coverm-strobealign-aemb-mapping-result")
+                .tempfile()
+                .unwrap_or_else(|_| panic!("Failed to create strobealign-aemb result tempfile"));
+            let mapping_log = tempfile::Builder::new()
+                .prefix("coverm-strobealign-aemb-mapping-log")
+                .tempfile()
+                .unwrap_or_else(|_| panic!("Failed to create strobealign-aemb log tempfile"));
+            let cmd = format!(
+                "strobealign --aemb -t {} {} {} {} > {} 2> {}",
+                threads,
+                p2.reference,
+                p2.read1,
+                p2.read2.unwrap_or(""),
+                mapping_result
+                    .path()
+                    .to_str()
+                    .expect("Failed to get strobealign-aemb result path"),
+                mapping_log
+                    .path()
+                    .to_str()
+                    .expect("Failed to get strobealign-aemb log path"),
+            );
+            log_files.push(mapping_log);
+            commands.push(cmd);
+        }
+    }
+
+    // Run each command in serial, and complete each process
+    // before starting the next one.
+    for cmd_string in commands {
+        debug!("Queuing cmd_string: {}", cmd_string);
+        let mut cmd = std::process::Command::new("bash");
+        cmd.arg("-c")
+            .arg(&cmd_string)
+            .stderr(std::process::Stdio::piped());
+        let process = cmd.spawn().expect("Unable to execute bash");
+        complete_processes(
+            vec![process],
+            vec![cmd_string],
+            vec!["strobealign-aemb log file".to_string()],
+            vec![log_files.remove(0)],
+            None,
+        );
+    }
+
+    // Read the mapping results and pass them to the coverage taker
+    panic!();
+}