--- a/cuffcompare_wrapper.py	Thu Jan 09 14:27:37 2014 -0500
+++ b/cuffcompare_wrapper.py	Fri Dec 19 11:55:55 2014 -0500
@@ -12,9 +12,17 @@
     #Parse Command Line
     parser = optparse.OptionParser()
     parser.add_option( '-r', dest='ref_annotation', help='An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.' )
-    parser.add_option( '-R', action="store_true", dest='ignore_nonoverlap', help='If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts accuracy file' )
+    parser.add_option( '-R', action="store_true", dest='ignore_nonoverlap_reference', help='If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts accuracy file' )
+    parser.add_option( '-Q', action="store_true", dest='ignore_nonoverlap_transfrag', help='If -r was specified, this option causes cuffcompare to consider only the input transcripts that overlap any of the reference transcripts (Sp correction); Warning: this will discard all "novel" loci!)' )
+
     parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.')
     
+    parser.add_option( '-M', action="store_true", dest='discard_single_exon_all', help='discard (ignore) single-exon transfrags and reference transcript')
+    parser.add_option( '-N', action="store_true", dest='discard_single_exon_ref', help='discard (ignore) single-exon reference transcripts')
+    parser.add_option( '-e', dest='max_dist_exon', help='Max. Distance for assessing exon accuracy" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100')
+    parser.add_option( '-d', dest='max_dist_group', help='Max.Distance for transcript grouping" help="max. distance (range) for grouping transcript start sites. Default: 100')
+    parser.add_option( '-F', action="store_true", dest='discard_redundant_intron_transfrags', help='Discard intron-redundant transfrags if they share the 5-prime end (if they differ only at the 3-prime end)')
+
     # Wrapper / Galaxy options.
     parser.add_option( '', '--index', dest='index', help='The path of the reference genome' )
     parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
@@ -63,11 +71,22 @@
     # Add options.
     if options.ref_annotation:
         cmd += " -r %s " % options.ref_annotation
-    if options.ignore_nonoverlap:
+    if options.ignore_nonoverlap_reference:
         cmd += " -R "
+    if options.ignore_nonoverlap_transfrag:
+	cmd += " -Q "
     if options.use_seq_data:
         cmd += " -s %s " % seq_path
-        
+    if options.discard_single_exon_all:
+	cmd += " -M "
+    if options.discard_single_exon_ref:
+	cmd += " -N "
+    if options.max_dist_exon:
+	cmd += " -e %i " % int( options.max_dist_exon )
+    if options.max_dist_group:
+	cmd += " -d %i " % int( options.max_dist_group )
+    if options.discard_redundant_intron_transfrags: 
+	cmd += " -F "
     # Add input files.
         
     # Need to symlink inputs so that output files are written to temp directory.