refactor: extract configuration, remove dead code

enclone/Cargo.toml

@@ -38,9 +38,6 @@ string_utils = { path = "../string_utils" }
 vdj_ann = { path = "../vdj_ann" }
 vector_utils = { path = "../vector_utils" }
 
-[target.'cfg(not(windows))'.dependencies]
-pager = "0.16"
-
 [target.'cfg(not(windows))'.dependencies.hdf5]
 git = "https://github.com/10XGenomics/hdf5-rust.git"
 branch = "conda_nov2021"

enclone/src/UNDOC_OPTIONS

@@ -48,16 +48,13 @@ Optional arguments governing input and output files:
 Optional arguments that control printing of individual clonotypes:
 
 - white   = percent of sequences implicated in whitelist expansion.
-- CHAIN_BRIEF: show abbreviated chain column headers
 - DEBUG_TABLE_PRINTING: add print lines to help debug printing of tables.
 - NOTE_SIMPLE: note if the first sequence for the chain is simple, in the sense that it exactly
                equals the concatenation of the right-truncated V with the full J segment.
 
 Other optional arguments:
 
 - FORCE: make joins even if redundant
-- EXP: exploratory code for exact clonotyping on
-- WEAK: for EXP, print all and show weaks
 - GRAPH: show logging from light-heavy graph construction
 - UTR_CON: run experimental UTR consensus code
 - CON_CON: run experimental constant region consensus code
@@ -67,7 +64,6 @@ Other optional arguments:
       2. You want to see the effect of changed annotation code.
 - NPLAIN: reverses PLAIN
 - INDELS: search for and list CDR3s from clonotypes with possible SHM indels (exploratory)
-- NOPRETTY: turn off pretty trace entirely
 - HEAVY_CHAIN_REUSE: look for instances of heavy chain reuse
 - BINARY=filename: generate binary output file
 - PROTO=filename: generate proto output file
@@ -83,13 +79,6 @@ 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/src/graph_filter.rs

@@ -3,7 +3,7 @@
 // This file provides the single function graph_filter.
 
 use enclone_core::barcode_fate::BarcodeFate;
-use enclone_core::defs::{EncloneControl, TigData};
+use enclone_core::defs::TigData;
 use enclone_core::enclone_structs::BarcodeFates;
 use graph_simple::GraphSimple;
 use io_utils::fwriteln;
@@ -32,9 +32,9 @@ use vector_utils::{bin_member, bin_position, erase_if, lower_bound, next_diff12_
 // Hmm, seems like the edges go from heavy to light.
 
 pub fn graph_filter(
-    ctl: &EncloneControl,
     tig_bc: &mut Vec<Vec<TigData>>,
-    graph: bool,
+    skip_graph_filter: bool,
+    log_graph: bool,
     fate: &mut [BarcodeFates],
 ) {
     let mut ndels = 0;
@@ -322,7 +322,7 @@ pub fn graph_filter(
                     && (stats[i].0).0 <= MAX_KILL_HEAVY
                     && (stats[i].0).1 <= MAX_KILL_HEAVY_CELLS
                 {
-                    if graph {
+                    if log_graph {
                         let w = stats[i].1;
                         println!(
                             "\nkill type 3, from {} to {}\nkilled by {} to {}",
@@ -379,10 +379,10 @@ pub fn graph_filter(
                 .insert(tig_bc[i][0].barcode.clone(), BarcodeFate::GraphFilter);
         }
     }
-    if !ctl.gen_opt.ngraph_filter {
+    if !skip_graph_filter {
         erase_if(tig_bc, &to_delete);
     }
-    if graph {
+    if log_graph {
         fwriteln!(log, "");
         print!("{}", strme(&log));
         println!("total graph filter deletions = {ndels}");

enclone/src/info.rs

@@ -222,10 +222,6 @@ pub fn build_info(
                 } else {
                     // maybe can't happen
                     vs.push(rt.clone());
-                    // At one point there was a bug in which the following line was missing.
-                    // This caused a traceback on "enclone 123085 RE".  It is interesting because
-                    // the traceback did not get back to the main program, even with
-                    // "enclone 123085 RE NOPRETTY".
                     vs_notes.push(String::new());
                     vsnx = String::new();
                 }

enclone/src/misc1.rs

@@ -4,13 +4,11 @@
 
 use enclone_core::{
     barcode_fate::BarcodeFate,
-    defs::{CloneInfo, EncloneControl, ExactClonotype, TigData},
+    defs::{CloneInfo, EncloneControl, ExactClonotype, OriginInfo, TigData},
     enclone_structs::BarcodeFates,
 };
 use equiv::EquivRel;
 use itertools::Itertools;
-#[cfg(not(target_os = "windows"))]
-use pager::Pager;
 
 use std::time::Instant;
 use string_utils::stringme;
@@ -20,44 +18,6 @@ use vector_utils::{
 
 // ▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓
 
-// This section contains a function that supports paging.  It does not work under Windows, and
-// we describe here all the *known* problems with getting enclone to work under Windows.
-// 1. It does not compile for us.  When we tried, there was a problem with libhdf-5.
-// 2. Paging is turned off, because the pager crate doesn't compile under Windows, and porting
-//    it to Windows appears nontrivial.
-// 3. ANSI escape characters are not handled correctly, at least by default.
-// In addition, we have some concerns about what it would mean to properly test enclone on Windows,
-// given that some users might have older OS installs, and support for ANSI escape characters
-// appears to have been changed in 2018. This is not made easier by the Windows Subsystem for
-// Linux.
-
-#[cfg(not(target_os = "windows"))]
-pub fn setup_pager(pager: bool) {
-    // If the output is going to a terminal, set up paging so that output is in effect piped to
-    // "less -R -F -X -K".
-    //
-    // ∙ The option -R is used to render ANSI escape characters correctly.  We do not use
-    //   -r instead because if you navigate backwards in less -r, stuff gets screwed up,
-    //   which is consistent with the scary stuff in the man page for less at -r.  However -R will
-    //   not display all unicode characters correctly, so those have to be picked carefully,
-    //   by empirically testing that e.g. "echo ◼ | less -R -F -X" renders correctly.
-    //
-    // ∙ The -F option makes less exit immediately if all the output can be seen in one screen.
-    //
-    // ∙ The -X option is needed because we found that in full screen mode on OSX Catalina, output
-    //   was sent to the alternate screen, and hence it appeared that one got no output at all
-    //   from enclone.  This is really bad, so do not turn off this option!
-
-    if pager {
-        Pager::with_pager("less -R -F -X -K").setup();
-    }
-}
-
-#[cfg(target_os = "windows")]
-pub fn setup_pager(_pager: bool) {}
-
-// ▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓
-
 // Lookup for heavy chain reuse (special purpose experimental option).
 // This is interesting but not likely to yield interesting examples of heavy chain reuse
 // because biologically it doesn't make sense that one would have both H-L1 and H-L2 expanded.
@@ -196,34 +156,34 @@ pub fn lookup_heavy_chain_reuse(
 // subsequently distintegrated.
 
 pub fn cross_filter(
-    ctl: &EncloneControl,
+    origin_info: &OriginInfo,
     tig_bc: &mut Vec<Vec<TigData>>,
     fate: &mut [BarcodeFates],
+    ncross: bool,
 ) {
     // Get the list of dataset origins.  Here we allow the same origin name to have been used
     // for more than one donor, as we haven't explicitly prohibited that.
 
     let mut origins = Vec::<(&str, &str)>::new();
-    for i in 0..ctl.origin_info.n() {
+    for i in 0..origin_info.n() {
         origins.push((
-            ctl.origin_info.donor_id[i].as_str(),
-            ctl.origin_info.origin_id[i].as_str(),
+            origin_info.donor_id[i].as_str(),
+            origin_info.origin_id[i].as_str(),
         ));
     }
     unique_sort(&mut origins);
-    let to_origin = ctl
-        .origin_info
+    let to_origin = origin_info
         .donor_id
         .iter()
-        .zip(ctl.origin_info.origin_id.iter())
+        .zip(origin_info.origin_id.iter())
         .map(|(donor_id, origin_id)| {
             bin_position(&origins, &(donor_id.as_str(), origin_id.as_str())) as usize
         })
         .collect::<Vec<_>>();
 
     // For each dataset index, and each origin, compute the total number of productive pairs.
 
-    let mut n_dataset_index = vec![0; ctl.origin_info.n()];
+    let mut n_dataset_index = vec![0; origin_info.n()];
     let mut n_origin = vec![0; origins.len()];
     for tigi in tig_bc.iter() {
         for x in tigi {
@@ -288,12 +248,12 @@ pub fn cross_filter(
         for tig in tigi {
             if tig.umi_count < UMIS_SAVE && bin_member(&blacklist, &tig.seq()) {
                 fate[tigi[0].dataset_index].insert(tigi[0].barcode.clone(), BarcodeFate::Cross);
-                if !ctl.clono_filt_opt_def.ncross {
-                    to_delete[i] = true;
-                }
+                to_delete[i] = true;
                 break;
             }
         }
     }
-    erase_if(tig_bc, &to_delete);
+    if !ncross {
+        erase_if(tig_bc, &to_delete);
+    }
 }