From: Diane Trout <diane@caltech.edu>
Date: Tue, 16 Nov 2010 01:41:04 +0000 (-0800)
Subject: Map junctions.bed to the Junctions view.
X-Git-Tag: 0.5.0~9
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=6d1e134c0f3755940189bbd1ed3f00957370479a

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 37ef731..72d7f32 100755
--- 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'),