From: Diane Trout <diane@ghic.org>
Date: Thu, 17 Oct 2013 22:03:43 +0000 (-0700)
Subject: Merge branch 'master' into django1.4
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=aa47067f5a80eef8eccd50b3c0f478f79cf0caf8;hp=-c

Merge branch 'master' into django1.4
---

aa47067f5a80eef8eccd50b3c0f478f79cf0caf8
diff --combined htsworkflow/pipelines/genomemap.py
index 1dd95df,4dbbc2d..6dfcf68
--- a/htsworkflow/pipelines/genomemap.py
+++ b/htsworkflow/pipelines/genomemap.py
@@@ -3,7 -3,7 +3,7 @@@
  from glob import glob
  import os
  import collections
 -from htsworkflow.pipelines.runfolder import ElementTree
 +from htsworkflow.pipelines import ElementTree
  
  vldInfo = collections.namedtuple('vldInfo', 'name is_link')
  
@@@ -77,13 -77,15 +77,15 @@@ def guess_genome(contig_sizes)
      # guess genome names
  
      genomes = {'chr1': {197195432: 'mm9',
-                         247249719: 'hg19',
+                         247249719: 'hg18',
                          200994015: 'galGal3',
+                         230208: 'saccer1',
                          },
                 'chrI': {230218: 'sacCer3',
                          15072421: 'elegans190'},
                 '1': {60348388: 'danRe6'},
-                'chr2L': { 23011544: 'dm3' },
+                'chr2L': { 23011544: 'dm3',
+                           49364326: 'Anopheles_gambiae'},
  
                 }