details: http://www.bx.psu.edu/hg/galaxy/rev/cd366f615220 changeset: 2491:cd366f615220 user: Dan Blankenberg dan@bx.psu.edu date: Thu Jul 23 11:11:41 2009 -0400 description: No longer guess the name column in interval set_meta(). Name column must now always be set manually.

1 file(s) affected in this change:

lib/galaxy/datatypes/interval.py

diffs (24 lines):

diff -r 3851029eda94 -r cd366f615220 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Wed Jul 22 21:28:26 2009 -0400 +++ b/lib/galaxy/datatypes/interval.py Thu Jul 23 11:11:41 2009 -0400 @@ -115,12 +115,14 @@ dataset.metadata.endCol = 3 except: pass # Metadata default will be used - if len( elems ) > 3: - try: - int( elems[3] ) - except: - if overwrite or not dataset.metadata.element_is_set( 'nameCol' ): - dataset.metadata.nameCol = 4 + #we no longer want to guess that this column is the 'name', name must now be set manually for interval files + #we will still guess at the strand, as we can make a more educated guess + #if len( elems ) > 3: + # try: + # int( elems[3] ) + # except: + # if overwrite or not dataset.metadata.element_is_set( 'nameCol' ): + # dataset.metadata.nameCol = 4 if len( elems ) < 6 or elems[5] not in data.valid_strand: if overwrite or not dataset.metadata.element_is_set( 'strandCol' ): dataset.metadata.strandCol = 0