fixed racing condition

scripts/launch_varscan.pl

@@ -99,7 +99,8 @@ sub mpileup{
 
   # Multithread a pileup so that each region gets piped into a file.
   # Then, these individual files can be combined at a later step.
-  my $command="echo \"$regions\" | xargs -P $$settings{numcpus} -n 1 -I {} sh -c 'echo \"MPileup on {}\" >&2; rm -fv $$settings{tempdir}/$b.*.mpileup >&2; samtools mpileup -f $reference $xopts --region \"{}\" $bam > $$settings{tempdir}/$b.\$\$.mpileup' ";
+  system("rm -fv $$settings{tempdir}/$b.*.mpileup >&2");
+  my $command="echo \"$regions\" | xargs -P $$settings{numcpus} -n 1 -I {} sh -c 'echo \"MPileup on {}\" >&2; samtools mpileup -f $reference $xopts --region \"{}\" $bam > $$settings{tempdir}/$b.\$\$.mpileup' ";
   logmsg "Running mpileup:\n  $command";
   system($command);
   die "ERROR with xargs and samtools mpileup" if $?;