revert

stjude-rust-labs · Dec 15, 2023 · 520ae46 · 520ae46
1 parent 9b45316
commit 520ae46
Show file tree

Hide file tree

Showing 3 changed files with 26 additions and 14 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -19,6 +19,7 @@ git-testament = "0.2.1"
 indexmap = "1.9.1"
 indicatif = "0.16.2"
 itertools = "0.10.5"
+lazy_static = "1.4.0"
 noodles = { version = "0.34.0", features = [
     "async",
     "bam",

diff --git a/src/derive/endedness/compute.rs b/src/derive/endedness/compute.rs
@@ -1,16 +1,23 @@
 //! Module holding the logic for computing the endedness of a BAM.
 
+use anyhow::bail;
+use lazy_static::lazy_static;
 use noodles::sam::header;
 use serde::Serialize;
 use std::collections::HashMap;
 use std::collections::HashSet;
+use std::sync::Arc;
 use tracing::warn;
 
-/// String used to index into the HashMaps used to store the "overall" ordering flags.
-pub static OVERALL: &str = "overall";
+// Strings used to index into the HashMaps used to store the Read Group ordering flags.
+// Lazy statics are used to save memory.
+lazy_static! {
+    /// String used to index into the HashMaps used to store the "overall" ordering flags.
+    pub static ref OVERALL: Arc<String> = Arc::new(String::from("overall"));
 
-/// String used to index into th HashMaps used to store the "unknown_read_group" ordering flags.
-pub static UNKNOWN_READ_GROUP: &str = "unknown_read_group";
+    /// String used to index into th HashMaps used to store the "unknown_read_group" ordering flags.
+    pub static ref UNKNOWN_READ_GROUP: Arc<String> = Arc::new(String::from("unknown_read_group"));
+}
 
 /// Struct holding the ordering flags for a single read group.
 #[derive(Debug, Clone)]
@@ -232,7 +239,10 @@ fn calculate_reads_per_template<'rg>(
         }
     }
 
-    reads_per_template.insert(OVERALL, total_reads as f64 / total_templates as f64);
+    reads_per_template.insert(
+        OVERALL.as_str(),
+        total_reads as f64 / total_templates as f64,
+    );
 
     for (read_group, num_reads) in read_group_reads.iter() {
         let num_templates = read_group_templates.get(read_group).unwrap();
@@ -362,7 +372,7 @@ pub fn predict(
     );
 
     for (read_group, rg_ordering_flags) in ordering_flags.iter() {
-        if (*read_group == UNKNOWN_READ_GROUP)
+        if (*read_group == UNKNOWN_READ_GROUP.as_str())
             && (rg_ordering_flags.first == 0
                 && rg_ordering_flags.last == 0
                 && rg_ordering_flags.both == 0
@@ -401,7 +411,7 @@ mod tests {
     fn test_predict_endedness() {
         let mut ordering_flags: HashMap<&str, OrderingFlagsCounts> = HashMap::new();
         ordering_flags.insert(
-            OVERALL,
+            OVERALL.as_str(),
             OrderingFlagsCounts {
                 first: 1,
                 last: 1,
@@ -411,7 +421,7 @@ mod tests {
         );
         let result = predict_endedness(
             "overall".to_string(),
-            &ordering_flags.get(OVERALL).unwrap(),
+            &ordering_flags.get(OVERALL.as_str()).unwrap(),
             0.0,
             None,
             false,
@@ -449,7 +459,7 @@ mod tests {
     fn test_derive_endedness_from_only_first() {
         let mut ordering_flags: HashMap<&str, OrderingFlagsCounts> = HashMap::new();
         ordering_flags.insert(
-            OVERALL,
+            OVERALL.as_str(),
             OrderingFlagsCounts {
                 first: 1,
                 last: 0,
@@ -472,7 +482,7 @@ mod tests {
     fn test_derive_endedness_from_only_last() {
         let mut ordering_flags: HashMap<&str, OrderingFlagsCounts> = HashMap::new();
         ordering_flags.insert(
-            OVERALL,
+            OVERALL.as_str(),
             OrderingFlagsCounts {
                 first: 0,
                 last: 1,
@@ -495,7 +505,7 @@ mod tests {
     fn test_derive_endedness_from_only_both() {
         let mut ordering_flags: HashMap<&str, OrderingFlagsCounts> = HashMap::new();
         ordering_flags.insert(
-            OVERALL,
+            OVERALL.as_str(),
             OrderingFlagsCounts {
                 first: 0,
                 last: 0,
@@ -518,7 +528,7 @@ mod tests {
     fn test_derive_endedness_from_only_neither() {
         let mut ordering_flags: HashMap<&str, OrderingFlagsCounts> = HashMap::new();
         ordering_flags.insert(
-            OVERALL,
+            OVERALL.as_str(),
             OrderingFlagsCounts {
                 first: 0,
                 last: 0,
@@ -541,7 +551,7 @@ mod tests {
     fn test_derive_endedness_from_first_and_last() {
         let mut ordering_flags: HashMap<&str, OrderingFlagsCounts> = HashMap::new();
         ordering_flags.insert(
-            OVERALL,
+            OVERALL.as_str(),
             OrderingFlagsCounts {
                 first: 1,
                 last: 1,
@@ -583,7 +593,7 @@ mod tests {
         let rg_paired = "rg_paired";
         let rg_single = "rg_single";
         ordering_flags.insert(
-            OVERALL,
+            OVERALL.as_str(),
             OrderingFlagsCounts {
                 first: 8,
                 last: 8,