From 60cf6775c20dbc2ee2bc0797c14b27c7d1c99ab6 Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Mon, 26 Sep 2022 14:25:30 -0500
Subject: [PATCH] notes toward command line read depth option

---
 src/main/java/CommandLineInterface.java | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/main/java/CommandLineInterface.java b/src/main/java/CommandLineInterface.java
index 1bf4dbc..4cac761 100644
--- a/src/main/java/CommandLineInterface.java
+++ b/src/main/java/CommandLineInterface.java
@@ -35,6 +35,10 @@ import java.util.stream.Stream;
  * output : name of the output file
  * graphml : output a graphml file
  * binary : output a serialized binary object file
+ * IF SIMULATING READ DEPTH, ALL THESE ARE REQUIRED. Absence indicates not simulating read depth
+ * readdepth: number of reads per sequence
+ * readerrorprob: probability of reading a sequence incorrectly
+ * errcollisionprob: probability of two read errors being identical
  *
  * Match flags:
  * graphFile : name of graph and data file to use as input