external_command_checker: Use crate which.

Suggested by: @nickp60

#207

Cargo.toml

@@ -15,21 +15,22 @@ default-run = "coverm"
 
 [dependencies]
 bio = "1.1.0"
-rust-htslib = { version="0.44.*", default-features = false }
+rust-htslib = { version="0.46.*", default-features = false }
 clap = { version="4.*", features = ["cargo"] } # cargo feature required for crate_version!
 clap_complete = "4.*"
 log = "0.4.*"
-env_logger = "0.10.*"
+env_logger = "0.11.*"
 nix = "0.26.*"
 tempdir = "0.3.*"
 tempfile = "3.*"
 ansi_term = "0.12"
 lazy_static = "1.4.0"
 rand = "0.8.*"
 serde = "1.0"
-version-compare = "0.1.0"
-bird_tool_utils = "0.5.0"
-# bird_tool_utils = { git = "https://github.com/wwood/bird_tool_utils" }
+version-compare = "0.2.0"
+# bird_tool_utils = "0.5.0"
+bird_tool_utils = { git = "https://github.com/wwood/bird_tool_utils" }
+# bird_tool_utils = { path = "../bird_tool_utils" }
 galah = "0.4.0"
 # galah = { git = "https://github.com/wwood/galah" }
 bird_tool_utils-man = "0.4.0"

src/external_command_checker.rs

@@ -1,32 +1,31 @@
 use bird_tool_utils::external_command_checker::*;
 
 pub fn check_for_bwa() {
-    check_for_external_command_presence("BWA", "which bwa").expect("Failed to find installed BWA");
+    check_for_external_command_presence_with_which("bwa").expect("Failed to find installed BWA");
 }
 
 pub fn check_for_bwa_mem2() {
-    check_for_external_command_presence("BWA", "which bwa-mem2")
-        .expect("Failed to find installed BWA");
+    check_for_external_command_presence_with_which("bwa").expect("Failed to find installed BWA");
     default_version_check("bwa-mem2", "2.0", false, Some("bwa-mem2 version"))
         .expect("Failed to find sufficient version of bwa-mem2");
 }
 
 pub fn check_for_minimap2() {
-    check_for_external_command_presence("minimap2", "which minimap2")
+    check_for_external_command_presence_with_which("minimap2")
         .expect("Failed to find installed minimap2");
     default_version_check("minimap2", "2.24-r1122", false, None)
         .expect("Failed to find sufficient version of minimap2");
 }
 
 pub fn check_for_samtools() {
-    check_for_external_command_presence("samtools", "which samtools")
+    check_for_external_command_presence_with_which("samtools")
         .expect("Failed to find installed samtools");
     default_version_check("samtools", "1.9", false, None)
         .expect("Failed to find sufficient version of samtools");
 }
 
 pub fn check_for_strobealign() {
-    check_for_external_command_presence("strobealign", "which strobealign")
+    check_for_external_command_presence_with_which("strobealign")
         .expect("Failed to find installed strobealign");
     default_version_check("strobealign", "0.11.0", false, None)
         .expect("Failed to find sufficient version of strobealign");