Change over from wiggle files to bedgraph files to profile reads. Reasons are

1) Wiggle files at some point exceed the amount of data that ucsc will accept
2) Bedgraph is more accurate, I think
3) Also, used this as an opportunity to put strand direction on profiles, so now two tracks
   are made, one for forward strand reads, one for reverse strand reads.

diff --git a/htswanalysis/scripts/ConfigureTasks.pm b/htswanalysis/scripts/ConfigureTasks.pm
index d4348c8b25b10273ac9a0141740909de24d384ea..183d0607ac762d3aa9968ffd2ece8bfd495384fc 100755 (executable)
--- a/htswanalysis/scripts/ConfigureTasks.pm
+++ b/htswanalysis/scripts/ConfigureTasks.pm
@@ -235,7 +235,7 @@ sub WriteProfileTasks {
 
       my $seqcheck = "if [ ! -e $data_dir/Libraries/$lib.txt ]; then $root_dir/scripts/analys_track_main.py updsts $task \"Waiting for sequencing.\"; fi;"; 
       my $cmds .= "$lib.wig.gz: $data_dir/Libraries/$lib.txt\n";
-      $cmds .= "\t".$PROFILEDIR.'/profile_reads_wig '.$data_dir.'/Libraries/'.$lib.'.txt "'.$name.'" "'.$name.'" | gzip > '.$lib.'.wig.gz';
+      $cmds .= "\t".$PROFILEDIR.'/profile_reads_bedgraph '.$data_dir.'/Libraries/'.$lib.'.txt "'.$name.'" "'.$name.'" | grep -v contam | grep -v Ribo | grep -v splice | gzip > '.$lib.'.wig.gz';
       $cmds .= "\n\n";
       $cmds .= $lib.'.profile.gif: '.$data_dir.'/Libraries/'.$lib.'.txt '.$root_dir.'/reference_data/'.$genome.'_tx_start_sites'."\n";
       $cmds .= "\t".$PROFILEDIR.'/profile_reads_against_features $^ | '.$root_dir.'/scripts/profile_to_svg.pm | /opt/local/bin/convert - $@'."\n";