Default max coverage to 50x for hifi datasets

marbl · Feb 25, 2020 · 7ce4846 · 7ce4846
1 parent d521766
commit 7ce4846
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/src/pipelines/canu.pl b/src/pipelines/canu.pl
@@ -403,8 +403,6 @@
 #  Fail if any thing flagged an error condition;
 
 configureAssembler();  #  Set job sizes and etc bases on genomeSize and hosts available.
-checkParameters();     #  Check all parameters (except error rates) are valid and consistent.
-printHelp();           #  And one final last chance to fail.
 
 #  Make space for us to work in, and move there.
 
@@ -627,6 +625,7 @@
     setGlobalIfUndef("utgErrorRate",     0.010);
     setGlobalIfUndef("cnsErrorRate",     0.050);
     setGlobalIfUndef("homoPolyCompress", 1);
+    setGlobalIfUndef("maxInputCoverage", 50);
     setGlobalIfUndef("batOptions",       "-eg 0.0003 -sb 0.01 -dg 0 -db 3 -dr 0 -ca 50 -cp 5");
 }
 
@@ -643,6 +642,9 @@
     $mode = "assemble"       if ($numCorTri > 0);
 }
 
+checkParameters();     #  Check all parameters (except error rates) are valid and consistent.
+printHelp();           #  And one final last chance to fail.
+
 ################################################################################
 
 #  Go!

diff --git a/src/pipelines/canu/Defaults.pm b/src/pipelines/canu/Defaults.pm
@@ -920,7 +920,7 @@ sub setDefaults () {
     setDefault("maxThreads",           undef,     "Maximum number of compute threads to use by any component of the assembler");
 
     setDefault("minInputCoverage",     10,        "Stop if input coverage is too low; default 10");
-    setDefault("maxInputCoverage",     200,       "If input coverage is high, downsample to something reasonable; default 200");
+    setDefault("maxInputCoverage",     undef,     "If input coverage is high, downsample to something reasonable; default 200");
 
     #####  Stopping conditions
 
@@ -1556,7 +1556,10 @@ sub checkParameters () {
         print STDERR "--  WARNING:  'readSamplingCoverage' will be removed in the next release.\n";
         print STDERR "--\n";
 
-        setGlobal("maxInputCoverage", getGlobal("readSamplingBias"));
+        setGlobal("maxInputCoverage", getGlobal("readSamplingCoverage"));
+    }
+    if (!defined(getGlobal("maxInputCoverage"))) {
+       setGlobal("maxInputCoverage", 200);
     }
     if (getGlobal("maxInputCoverage") eq "all") {
         setGlobal("maxInputCoverage", 0);
@@ -1574,7 +1577,6 @@ sub checkParameters () {
         addCommandLineError("ERROR:  stopOnLowCoverage ($minc) must be less than maxInputCoverage ($maxc).\n");
     }
 
-
     if ((getGlobal("saveOverlaps") ne "0") &&
         (getGlobal("saveOverlaps") ne "1")) {
         addCommandLineError("ERROR:  Invalid 'saveOverlaps' specified (" . getGlobal("saveOverlaps") . "); must be 'true' or 'false'\n");