From 451eaa56e3e2fbe34db4d995188110f45938224d Mon Sep 17 00:00:00 2001
From: Lee Katz - Aspen <gzu2@cdc.gov>
Date: Wed, 2 Sep 2015 11:31:44 -0400
Subject: [PATCH] some filename fixes and better logmsg

---
 scripts/shuffleSplitReads.pl | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/scripts/shuffleSplitReads.pl b/scripts/shuffleSplitReads.pl
index 80f4741..f9ff173 100755
--- a/scripts/shuffleSplitReads.pl
+++ b/scripts/shuffleSplitReads.pl
@@ -84,11 +84,14 @@ sub shuffleWorker{
   while(defined(my $tmp=$Q->dequeue)){
     my($basename,$reads)=@$tmp;
 
-    logmsg "Looking for $basename";
-    my $outfile="$outdir/$basename.fastq.gz";
-    next if(-e $outfile);
-
-    system("run_assembly_shuffleReads.pl $$reads{1} $$reads{2} | gzip -c > $outfile.tmp");
+    my $outfile="$outdir/".basename($basename).".fastq.gz";
+    logmsg "Looking for $basename*";
+    if(-e $outfile){
+      logmsg "Found $outfile; will not reshuffle";
+      next;
+    }
+    my $command="run_assembly_shuffleReads.pl $$reads{1} $$reads{2} | gzip -c > $outfile.tmp";
+    system($command);
     die "ERROR with run_assembly_shuffleReads.pl" if $?;
     system("mv -v $outfile.tmp $outfile");
   }