Map junctions.bed to the Junctions view.

Hopefully it'll pass validation and not be treated as a bed file,
even though it ends in the .bed extension.

(There were lots of problems with a previous subission because the
cufflinks bed file was almost but not quite a match to ucsc's bed
file validator. Or maybe they caved on the definition of a score.)

diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py
index 37ef73193f0ae98f680b9dfba6e3463b029a8feb..72d7f325e64b9d91966cf603dbd1a7236d683add 100755 (executable)
--- a/extra/ucsc_encode_submission/ucsc_gather.py
+++ b/extra/ucsc_encode_submission/ucsc_gather.py
@@ -596,6 +596,7 @@ class NameToViewMap(object):
             ('*.bai',                   None),
             ('*.bam',                   self._guess_bam_view),
             ('*.splices.bam',           'Splices'),
+            ('junctions.bed',           'Junctions'),
             ('*.jnct',                  'Junctions'),
             ('*.plus.bigwig',           'PlusSignal'),
             ('*.minus.bigwig',          'MinusSignal'),