Only set the error rate based on read type if it hasn't been set via …

…the command line.
sgblanch · Dec 13, 2016 · 7b04cd0 · 7b04cd0
1 parent a07ceea
commit 7b04cd0
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Showing 3 changed files with 16 additions and 11 deletions.
diff --git a/src/pipelines/canu.pl b/src/pipelines/canu.pl
@@ -227,10 +227,10 @@
     $haveCorrected = 1                  if ($type =~ m/corrected/);
     $haveRaw = 1                        if ($type =~ m/raw/);
 
-    setErrorRate(0.015)                 if ($type =~ m/pacbio/);
+    setErrorRate(0.015, 0)              if ($type =~ m/pacbio/);
     setGlobal("corErrorRate", "0.30")   if ($type =~ m/pacbio/);
 
-    setErrorRate(0.048)                 if ($type =~ m/nanopore/);
+    setErrorRate(0.048, 0)              if ($type =~ m/nanopore/);
     setGlobal("corErrorRate", "0.50")   if ($type =~ m/nanopore/);
 }
 
@@ -251,7 +251,7 @@
 
     # set to the default if we can't find anything
     if (!defined($gkpStore)) {
-        setErrorRate(0.01);
+        setErrorRate(0.01, 0);
     } else {
         my $numPacBioRaw         = 0;
         my $numPacBioCorrected   = 0;
@@ -266,12 +266,12 @@
             $numNanoporeCorrected++   if (m/nanopore-corrected/);
         }
         if ($numPacBioRaw > 0 || $numPacBioCorrected > 0) {
-            setErrorRate(0.015);
+            setErrorRate(0.015, 0);
             setGlobal("corErrorRate", "0.30");
             setGlobal("cnsMaxCoverage", 40);
         }
         if ($numNanoporeRaw > 0 || $numNanoporeCorrected > 0) {
-            setErrorRate(0.048);
+            setErrorRate(0.048, 0);
             setGlobal("corErrorRate", "0.50");
             setGlobal("cnsMaxCoverage", 40);
         }

diff --git a/src/pipelines/canu/Defaults.pm b/src/pipelines/canu/Defaults.pm
@@ -131,7 +131,7 @@ sub setGlobal ($$) {
     return  if ($set > 0);
 
     if ($var eq "errorrate") {
-        setErrorRate($val);
+        setErrorRate($val, 1);
         return;
     }
 
@@ -533,11 +533,16 @@ sub showErrorRates ($) {
 #    trimming   errorRate = 0.009  obtOvlErrorRate = 0.06  obtErrorRate = 0.035
 #    assembly   errorRate = 0.009  utgOvlErrorRate = 0.06  bogart 0.035
 #
-sub setErrorRate ($@) {
+sub setErrorRate ($$) {
     my $er      = shift @_;
-    my $verbose = shift @_;
+    my $force   = shift @_;
 
-    print STDERR "-- Set errorRate to $er (verbose='$verbose')\n"  if (defined($verbose));
+    if (($force == 0) && (defined($global{"errorrate"}))) {
+        #print STDERR "-- Can't change error rate from ", getGlobal('errorRate'), " to $er - not allowed.\n";
+        return;
+    }
+
+    #print STDERR "-- Set errorRate to $er\n";
 
     #  Can NOT call setGlobal() for this, because it calls setErrorRate()!.
     $global{"errorrate"} = $er;
@@ -551,7 +556,7 @@ sub setErrorRate ($@) {
     #setGlobal("corErrorRate",       $er * 10);  #  Erorr rate used for raw sequence alignment/consensus
     setGlobal("cnsErrorRate",       $er * 3);
 
-    showErrorRates("--  ")  if (defined($verbose));
+    #showErrorRates("--  ");
 }
 
 

diff --git a/src/pipelines/canu/ErrorEstimate.pm b/src/pipelines/canu/ErrorEstimate.pm
@@ -252,7 +252,7 @@ sub estimateCorrectedError ($$$) {
     } else {
        print STDERR "-- Estimated error rate: " . ($errorRate * 100) . "%.\n";
     }
-    setErrorRate($errorRate);
+    setErrorRate($errorRate, 1);
     showErrorRates("--  ");
     print STDERR "-- \n";
 }