Restore unconditional filter and re-scope a few things.

enclone_print/src/print_clonotypes.rs

@@ -249,7 +249,7 @@ pub fn print_clonotypes(
 
         let mut stats_pass1 = Vec::<Vec<(String, Vec<String>)>>::new();
 
-        for _ in [0] {
+        let bads = (|| -> Result<_, String> {
             // pass 1
 
             // Sort exact subclonotypes.
@@ -329,9 +329,23 @@ pub fn print_clonotypes(
             if !(n >= ctl.clono_filt_opt.ncells_low
                 || ctl.clono_group_opt.asymmetric_center == "from_filters")
             {
-                continue;
+                return Ok(Vec::new());
             }
             {
+                // Mark some weak exact subclonotypes for deletion.
+                let mut bads = vec![false; exacts.len()];
+                delete_weaks(ctl, &exacts, exact_clonotypes, mat, refdata, &mut bads);
+
+                // Done unless on second pass.  Unless there are bounds or COMPLETE specified
+                // or VAR_DEF specified.
+
+                if ctl.clono_filt_opt.bounds.is_empty()
+                    && !ctl.gen_opt.complete
+                    && ctl.gen_opt.var_def.is_empty()
+                {
+                    return Ok(bads);
+                }
+
                 // Find variant positions.  And some other things.
 
                 let mut vars = Vec::<Vec<usize>>::new();
@@ -353,20 +367,6 @@ pub fn print_clonotypes(
                     &mut res.out_data,
                 );
 
-                // Mark some weak exact subclonotypes for deletion.
-                let mut bads = vec![false; exacts.len()];
-                delete_weaks(ctl, &exacts, exact_clonotypes, mat, refdata, &mut bads);
-
-                // Done unless on second pass.  Unless there are bounds or COMPLETE specified
-                // or VAR_DEF specified.
-
-                if ctl.clono_filt_opt.bounds.is_empty()
-                    && !ctl.gen_opt.complete
-                    && ctl.gen_opt.var_def.is_empty()
-                {
-                    continue;
-                }
-
                 // Define amino acid positions to show.
 
                 let show_aa = build_show_aa(
@@ -707,14 +707,17 @@ pub fn print_clonotypes(
 
                 process_complete(ctl, nexacts, &mut bads, mat);
 
-                // Delete weak exact subclonotypes.
-
-                if !ctl.clono_filt_opt.protect_bads {
-                    erase_if(&mut mults, &bads);
-                    erase_if(&mut exacts, &bads);
-                }
+                Ok(bads)
             }
-        } // end pass 1
+        })()?; // end pass 1
+
+        // Delete weak exact subclonotypes.
+
+        if !ctl.clono_filt_opt.protect_bads {
+            erase_if(&mut mults, &bads);
+            erase_if(&mut exacts, &bads);
+        }
+
         for _ in [0] {
             // pass 2