Fix default coverage subsampling for HiFi (e.g. #2241)

marbl · Jul 14, 2023 · e0ed3bb · e0ed3bb
1 parent e8c6822
commit e0ed3bb
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git 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
@@ -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);
     }