From fb47d4a01375131e701dc86f3472e7f834ea9bf2 Mon Sep 17 00:00:00 2001
From: "Brian P. Walenz" <thebri@gmail.com>
Date: Tue, 8 Aug 2017 07:58:58 -0400
Subject: [PATCH] Add corOutCoverage=all, where all is 9999.

---
 src/pipelines/canu/Defaults.pm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/pipelines/canu/Defaults.pm b/src/pipelines/canu/Defaults.pm
index 8716391d5..7806fde55 100644
--- a/src/pipelines/canu/Defaults.pm
+++ b/src/pipelines/canu/Defaults.pm
@@ -1200,7 +1200,10 @@ sub checkParameters () {
 
     foreach my $var ("corOutCoverage") {
         if (!defined(getGlobal($var))) {
-            addCommandLineError("ERROR:  Invalid 'corOutCoverage' specified (" . getGlobal("corOutCoverage") . "); must be at least 1.0\n");
+            addCommandLineError("ERROR:  Invalid 'corOutCoverage' specified; must be at least 1.0\n");
+        }
+        elsif (getGlobal($var) =~ m/all/i) {
+            setGlobal($var, 9999);
         }
         elsif (getGlobal($var) !~ m/^[.-0123456789]/) {
             addCommandLineError("ERROR:  Invalid '$var' specified (" . getGlobal("$var") . "); must be numeric\n");