Add a -V/--version flag and fix bigwigvaluesoverbed about.

bigtools/src/bin/bigtools.rs

@@ -42,57 +42,58 @@ struct ChromIntersectArgs {
 }
 
 #[derive(Clone, Debug, PartialEq, Subcommand)]
+#[command(version)]
 enum SubCommands {
     Intersect {
         #[command(flatten)]
         args: IntersectArgs,
     },
-    #[command(name = "chromintersect")]
+    #[command(name = "chromintersect", version)]
     ChromIntersect {
         #[command(flatten)]
         args: ChromIntersectArgs,
     },
-    #[command(name = "bedgraphtobigwig")]
+    #[command(name = "bedgraphtobigwig", version)]
     BedGraphToBigWig {
         #[command(flatten)]
         args: BedGraphToBigWigArgs,
     },
-    #[command(name = "bedtobigbed")]
+    #[command(name = "bedtobigbed", version)]
     BedToBigBed {
         #[command(flatten)]
         args: BedToBigBedArgs,
     },
-    #[command(name = "bigbedinfo")]
+    #[command(name = "bigbedinfo", version)]
     BigBedInfo {
         #[command(flatten)]
         args: BigBedInfoArgs,
     },
-    #[command(name = "bigbedtobed")]
+    #[command(name = "bigbedtobed", version)]
     BigBedToBed {
         #[command(flatten)]
         args: BigBedToBedArgs,
     },
-    #[command(name = "bigwigaverageoverbed")]
+    #[command(name = "bigwigaverageoverbed", version)]
     BigWigAverageOverBed {
         #[command(flatten)]
         args: BigWigAverageOverBedArgs,
     },
-    #[command(name = "bigwiginfo")]
+    #[command(name = "bigwiginfo", version)]
     BigWigInfo {
         #[command(flatten)]
         args: BigWigInfoArgs,
     },
-    #[command(name = "bigwigmerge")]
+    #[command(name = "bigwigmerge", version)]
     BigWigMerge {
         #[command(flatten)]
         args: BigWigMergeArgs,
     },
-    #[command(name = "bigwigtobedgraph")]
+    #[command(name = "bigwigtobedgraph", version)]
     BigWigToBedGraph {
         #[command(flatten)]
         args: BigWigToBedGraphArgs,
     },
-    #[command(name = "bigwigvaluesoverbed")]
+    #[command(name = "bigwigvaluesoverbed", version)]
     BigWigValuesOverBed {
         #[command(flatten)]
         args: BigWigValuesOverBedArgs,

bigtools/src/utils/cli.rs

@@ -140,7 +140,13 @@ pub fn compat_args(mut args: impl Iterator<Item = OsString>) -> impl Iterator<It
         .unwrap_or(false)
     {
         let second = args.next();
-        let second = second.map(|a| a.to_ascii_lowercase());
+        let second = second.map(|a| {
+            if a.eq_ignore_ascii_case("-V") {
+                a
+            } else {
+                a.to_ascii_lowercase()
+            }
+        });
         if let Some(command) = second
             .as_ref()
             .and_then(|f| Path::new(f).file_name())

bigtools/src/utils/cli/bigwigvaluesoverbed.rs

@@ -12,7 +12,7 @@ use crate::{BBIFileRead, BBIReadError};
 #[derive(Clone, Debug, PartialEq, Parser)]
 #[command(
     name = "bigwigvaluesoverbed",
-    about = "Converts a bed to a bigBed.",
+    about = "For each bed interval, gets the base-resolution values from a bigWig.",
     long_about = None,
 )]
 pub struct BigWigValuesOverBedArgs {