fix pool and pseudo

workflow/scripts/convert_reads.py

@@ -138,12 +138,11 @@ def main():
         utils.strip_extensions(bam, ['.bam', '.dedup']))
 
     tag_filename = bam_basename + '.tagAlign.gz'
+    convert_mapped(bam, tag_filename)
 
     if paired:  # paired-end data
-        convert_mapped(bam, tag_filename)
         convert_mapped_pe(bam, bam_basename, tag_filename)
     else:
-        convert_mapped(bam, tag_filename)
         bedse_filename = bam_basename + ".bedse.gz"
         shutil.copy(tag_filename, bedse_filename)