push doc changes

libradicl/src/quant.rs

@@ -11,18 +11,14 @@ extern crate petgraph;
 extern crate serde;
 extern crate slog;
 
-//use executors::crossbeam_channel_pool;
-//use executors::*;
-//use std::sync::mpsc::channel;
-
 use self::indicatif::{ProgressBar, ProgressStyle};
 use self::petgraph::prelude::*;
 #[allow(unused_imports)]
 use self::slog::crit;
 use self::slog::info;
 use crate as libradicl;
 use crossbeam_queue::ArrayQueue;
-//use crossbeam_channel::bounded;
+
 // use fasthash::sea;
 use needletail::bitkmer::*;
 use scroll::Pwrite;
@@ -47,6 +43,16 @@ use self::libradicl::utils::*;
 
 /// Extracts the parsimonious UMI graphs (PUGs) from the
 /// equivalence class map for a given cell.
+/// The returned graph is a directed graph (potentially with 
+/// bidirected edges) where each node consists of an (equivalence 
+/// class, UMI ID) pair.  Note, crucially, that the UMI ID is simply 
+/// the rank of the UMI in the list of all distinct UMIs for this 
+/// equivalence class.  There is a directed edge between any pair of 
+/// vertices whose set of transcripts overlap and whose UMIs are within
+/// a Hamming distance of 1 of each other.  If one node has more than 
+/// twice the frequency of the other, the edge is directed from the 
+/// more frequent to the less freuqent node.  Otherwise, edges are 
+/// added in both directions.
 fn extract_graph(
     eqmap: &EqMap,
     log: &slog::Logger,