From e0ed3bb4e61863250de78ad95ae51a176491b7d5 Mon Sep 17 00:00:00 2001
From: Sergey Koren <sergek@umd.edu>
Date: Fri, 14 Jul 2023 10:26:46 -0400
Subject: [PATCH] Fix default coverage subsampling for HiFi (e.g. #2241)

---
 src/pipelines/canu.pl          | 2 ++
 src/pipelines/canu/Defaults.pm | 3 ---
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/pipelines/canu.pl b/src/pipelines/canu.pl
index 50ab1c128..90b6cc968 100644
--- a/src/pipelines/canu.pl
+++ b/src/pipelines/canu.pl
@@ -614,6 +614,7 @@
     setGlobalIfUndef("oeaHaploConfirm",  5);
     setGlobalIfUndef("utgErrorRate",     0.120);
     setGlobalIfUndef("cnsErrorRate",     0.200);
+    setGlobalIfUndef("maxInputCoverage",   200);
 }
 
 if (($numPacBio    > 0) &&
@@ -628,6 +629,7 @@
     setGlobalIfUndef("oeaHaploConfirm",  5);
     setGlobalIfUndef("utgErrorRate",     0.045);
     setGlobalIfUndef("cnsErrorRate",     0.075);
+    setGlobalIfUndef("maxInputCoverage",   200);
 }
 
 if (($numPacBio   == 0) &&
diff --git a/src/pipelines/canu/Defaults.pm b/src/pipelines/canu/Defaults.pm
index 18954f5c9..e71416092 100644
--- a/src/pipelines/canu/Defaults.pm
+++ b/src/pipelines/canu/Defaults.pm
@@ -1554,9 +1554,6 @@ sub checkParameters () {
         addCommandLineError("ERROR:  Invalid 'cnsConsensus' specified (" . getGlobal("cnsConsensus") . "); must be 'quick', 'pbdagcon', or 'utgcns'\n");
     }
 
-    if (!defined(getGlobal("maxInputCoverage"))) {
-       setGlobal("maxInputCoverage", 200);
-    }
     if (getGlobal("maxInputCoverage") eq "all") {
         setGlobal("maxInputCoverage", 0);
     }