Fix 4 bugs found in deep audit

BamViewer:
- B1: Count cards showed truncated read counts (max 80) instead of real
  totals. Now uses view.counts from backend (all reads).
- B2: BamCell variant site coloring was case-sensitive — lowercase BAM
  bases didn't match uppercase VCF alleles. Now uses toUpperCase().

Backend:
- B3: ensure_fasta_index silently wrote corrupt .fai for gzipped FASTA
  (byte offsets meaningless in compressed files). Now returns error
  asking user to decompress first.

App.tsx:
- B4: Ctrl/Cmd+Enter shortcut bypassed overwrite conflict check, going
  directly to handleRunAll. Extracted shared triggerRun() function used
  by both the button onClick and keyboard shortcut. Both now check for
  existing files before running.

Author: Paururo

frontend/src/App.tsx

@@ -609,20 +609,46 @@ function App() {
   // Count pending + error samples (runnable)
   const runnableCount = samples.filter((s) => s.status === "pending" || s.status === "error").length;
 
+  // Shared run trigger — checks for overwrite conflicts before launching
+  const triggerRun = useCallback(async () => {
+    if (!filesReady || samples.length === 0) {
+      setShowValidation(true);
+      return;
+    }
+    setShowValidation(false);
+
+    if (runnableCount > 0) {
+      try {
+        const conflicts = await invoke<string[]>("check_output_conflicts", { config: configRef.current });
+        if (conflicts.length > 0) {
+          const names = conflicts.map((p: string) => p.split(/[\\/]/).pop()).join(", ");
+          const ok = window.confirm(
+            `The following output files already exist and will be overwritten:\n\n${names}\n\nContinue?`
+          );
+          if (!ok) return;
+        }
+      } catch {
+        // If check fails, proceed anyway
+      }
+      handleRunAll();
+    } else {
+      handleRerunAll();
+    }
+  }, [filesReady, samples.length, runnableCount, handleRunAll, handleRerunAll]);
+
   // Ctrl+Enter / Cmd+Enter shortcut to run analysis
-  // Use a ref to always capture the latest handleRunAll without re-registering the listener
-  const handleRunAllRef = useRef(handleRunAll);
-  handleRunAllRef.current = handleRunAll;
+  const triggerRunRef = useRef(triggerRun);
+  triggerRunRef.current = triggerRun;
   const runStateRef = useRef({ running, filesReady, runnableCount });
   runStateRef.current = { running, filesReady, runnableCount };
 
   useEffect(() => {
     const handler = (e: KeyboardEvent) => {
       if ((e.ctrlKey || e.metaKey) && e.key === "Enter") {
         e.preventDefault();
-        const { running: r, filesReady: f, runnableCount: rc } = runStateRef.current;
-        if (!r && f && rc > 0) {
-          handleRunAllRef.current();
+        const { running: r } = runStateRef.current;
+        if (!r) {
+          triggerRunRef.current();
         }
       }
     };
@@ -834,32 +860,7 @@ function App() {
                   <button
                     className={`run-button${justFinished ? " run-button--success" : ""}`}
                     disabled={running}
-                    onClick={async () => {
-                      if (!filesReady || samples.length === 0) {
-                        setShowValidation(true);
-                        return;
-                      }
-                      setShowValidation(false);
-
-                      // Check for existing output files before running
-                      if (runnableCount > 0) {
-                        try {
-                          const conflicts = await invoke<string[]>("check_output_conflicts", { config });
-                          if (conflicts.length > 0) {
-                            const names = conflicts.map((p) => p.split(/[\\/]/).pop()).join(", ");
-                            const ok = window.confirm(
-                              `The following output files already exist and will be overwritten:\n\n${names}\n\nContinue?`
-                            );
-                            if (!ok) return;
-                          }
-                        } catch {
-                          // If check fails, proceed anyway
-                        }
-                        handleRunAll();
-                      } else {
-                        handleRerunAll();
-                      }
-                    }}
+                    onClick={() => triggerRun()}
                   >
                     {justFinished ? (
                       <>

frontend/src/components/BamViewer.tsx

@@ -233,17 +233,18 @@ function BamCell({ value, position, referenceBase, site }: {
   const cls = ["bam-cell"];
   let text = value || "";
 
+  const uc = value?.toUpperCase() ?? "";
   if (!value) {
     cls.push("bam-cell--empty");
   } else if (site) {
     cls.push("bam-cell--focus");
-    if (value === site.altBase) cls.push("bam-cell--focus-alt");
-    else if (value === site.referenceBase) cls.push("bam-cell--focus-ref");
+    if (uc === site.altBase.toUpperCase()) cls.push("bam-cell--focus-alt");
+    else if (uc === site.referenceBase.toUpperCase()) cls.push("bam-cell--focus-ref");
     else if (value === "-") cls.push("bam-cell--focus-gap");
     else cls.push("bam-cell--focus-other");
   } else if (value === "-") {
     cls.push("bam-cell--gap");
-  } else if (value === referenceBase) {
+  } else if (uc === referenceBase.toUpperCase()) {
     cls.push("bam-cell--match");
     text = ""; // IGV-style: match = colored bar, no text
   } else {
@@ -507,14 +508,15 @@ export default function BamViewer({ bamPath, fastaPath, data, minMapq, minBaseQu
   }, [view]);
   const maxCoverage = useMemo(() => Math.max(1, ...coverageData), [coverageData]);
 
-  // Counts from the returned (truncated) reads — matches what's actually visible
+  // Use real counts from ALL reads (backend computes before truncation)
   const displayCounts = useMemo(() => {
     if (!view) return { mnv: 0, partial: 0, reference: 0, other: 0 };
-    const c = { mnv: 0, partial: 0, reference: 0, other: 0 };
-    for (const read of view.reads) {
-      if (read.support in c) c[read.support as keyof typeof c]++;
-    }
-    return c;
+    return {
+      mnv: view.counts.mnv,
+      partial: view.counts.partial,
+      reference: view.counts.reference,
+      other: view.counts.other,
+    };
   }, [view]);
 
   // Filtered reads by support type

src-tauri/src/commands.rs

@@ -198,6 +198,11 @@ pub fn ensure_fasta_index(fasta_path: String) -> Result<String, String> {
         return Ok(fai_path);
     }
 
+    // Cannot index gzipped FASTA — byte offsets would be meaningless
+    if fasta_path.ends_with(".gz") || fasta_path.ends_with(".bgz") {
+        return Err("Cannot create .fai index for gzipped FASTA. Please decompress first.".to_string());
+    }
+
     let bytes = std::fs::read(&fasta_path)
         .map_err(|e| format!("Cannot read FASTA: {}", e))?;