From c8f410665808aa9d1d572ab22182da509fb9c1a5 Mon Sep 17 00:00:00 2001 From: "Brian P. Walenz" Date: Fri, 8 Sep 2017 01:09:28 -0400 Subject: [PATCH] If the path is absolute, don't call abs_path(). Issue #616. --- src/pipelines/canu/Defaults.pm | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/src/pipelines/canu/Defaults.pm b/src/pipelines/canu/Defaults.pm index 4a27feac6..7c3ca5685 100644 --- a/src/pipelines/canu/Defaults.pm +++ b/src/pipelines/canu/Defaults.pm @@ -509,6 +509,7 @@ sub addSequenceFile ($$@) { return(undef) if (!defined($file)); # No file name? Nothing to do. $file = "$dir/$file" if (defined($dir)); # If $dir defined, assume file is in there. + return($file) if ($file =~ m!/!); # If already a full path, use that. return(abs_path($file)) if (-e $file); # If found, return the full path. # And if not found, report an error, unless told not to. This is because on the command @@ -921,7 +922,6 @@ sub setDefaults () { setDefault("corMinCoverage", undef, "Minimum number of bases supporting each corrected base, if less than this sequences are split; default based on input read coverage: 0 <= 30x < 4 < 60x <= 4"); setDefault("corFilter", "expensive", "Method to filter short reads from correction; 'quick' or 'expensive'; default 'expensive'"); setDefault("corConsensus", "falcon", "Which consensus algorithm to use; only 'falcon' is supported; default 'falcon'"); - setDefault("corLegacyFilter", undef, "Expert option: global filter, length * identity (default) or length with broken by identity (if on)"); # Convert all the keys to lowercase, and remember the case-sensitive version @@ -1358,14 +1358,6 @@ sub checkParameters () { addCommandLineError("contigFilter 'lowCovFraction' must be between 0.0 and 1.0, currently $v[3]\n") if (($v[3] < 0) || (1 < $v[3]) || ($v[3] !~ m/^[0-9]*\.{0,1}[0-9]*$/)); addCommandLineError("contigFilter 'lowCovDepth' must be a positive integer, currently $v[4]\n") if (($v[4] < 0) || ($v[4] !~ m/^[0-9]+$/)); } - - # - # Minimap, no valid identities, set legacy - # - - if (getGlobal("corOverlapper") eq "minimap") { - setGlobalIfUndef("corLegacyFilter", 1); - } }