Remove never-completed EXT functionality.

enclone/src/UNDOC_OPTIONS

@@ -80,13 +80,6 @@ expanded out.
 CELLRANGER: for use if called from cellranger -- changes failure message and prevents exit
             upon normal completion
 
-EXT=filename:
-Given output of an external clonotyping algorithm which took as inputs the pipeline outputs
-for the lenas in enclone.testdata, for each exact subclonotype found by enclone, report its
-composition in the external clonotyping, as clonotype_id[count], ...
-The input file should have lines of the form:
-sample barcode clonotype_id.
-
 SUMMARY_CLEAN: if SUMMARY specified, don't show computational performance stats, so
 we can regress on output
 

enclone_args/src/proc_args.rs

@@ -576,7 +576,6 @@ pub fn proc_args(ctl: &mut EncloneControl, args: &[String]) -> Result<(), String
         ("CLUSTAL_AA", &mut ctl.gen_opt.clustal_aa),
         ("CLUSTAL_DNA", &mut ctl.gen_opt.clustal_dna),
         ("CONFIG", &mut ctl.gen_opt.config_file),
-        ("EXT", &mut ctl.gen_opt.ext),
         ("GROUP_CDR3", &mut ctl.clono_group_opt.cdr3),
         ("PCHAINS", &mut ctl.parseable_opt.pchains),
         ("SESSION_NAME", &mut ctl.gen_opt.session_name),

enclone_core/src/defs.rs

@@ -288,8 +288,6 @@ pub struct GeneralOpt {
     pub h5_pre: bool,
     pub accept_reuse: bool,
     pub descrip: bool,
-    pub ext: String,
-    pub extn: HashMap<String, usize>,
     pub mouse: bool,
     pub noprint: bool,
     pub noprintx: bool,