--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cgatools/lib/galaxy/datatypes/completegenomics.py	Mon Jun 18 20:15:00 2012 -0400
@@ -0,0 +1,71 @@
+"""
+Complete Genomics datatypes
+Birgit Crain - Complete Genomics, Inc
+"""
+
+import pkg_resources
+pkg_resources.require( "bx-python" )
+
+import logging
+from galaxy.datatypes import data
+from galaxy import util
+from cgi import escape
+from galaxy.datatypes import metadata
+from galaxy.datatypes import tabular
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.tabular import Tabular
+import galaxy_utils.sequence.vcf
+from galaxy.datatypes.sniff import *
+
+log = logging.getLogger(__name__)
+
+class CG_Var( Tabular ):
+    file_ext = 'cg_var'
+    def __init__(self, **kwd):
+        """Initialize CG_Var datatype"""
+        Tabular.__init__( self, **kwd )
+        self.column_names = ['locus', 'ploidy', 'allele', 'chromosome', 'begin', 'end',
+                             'varType', 'reference', 'alleleSeq', 'varScoreVAF',
+                             'varScoreEAF', 'varQuality', 'hapLink', 'xRef'
+                             ]
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, column_names=self.column_names )
+
+class CG_MasterVar( Tabular ):
+    file_ext = 'cg_mastervar'
+    def __init__(self, **kwd):
+        """Initialize CG_MasterVar datatype"""
+        Tabular.__init__( self, **kwd )
+        self.column_names = ['locus', 'ploidy', 'chromosome', 'begin', 'end', 'zygosity',
+                             'varType', 'reference', 'allele1Seq', 'allele2Seq',
+                             'allele1VarScoreVAF', 'allele2VarScoreVAF', 'allele1VarScoreEAF',
+                             'allele2VarScoreEAF', 'allele1VarQuality', 'allele2VarQuality',
+                             'allele1HapLink', 'allele2HapLink', 'allele1XRef', 'allele2XRef',
+                             'evidenceIntervalId', 'allele1ReadCount', 'allele2ReadCount',
+                             'referenceAlleleRead', 'totalReadCount', 'allele1Gene',
+                             'allele2Gene	pfam', 'miRBaseId', 'repeatMasker', 'segDupOverlap',
+                             'relativeCoverageDiploid', 'calledPloidy',
+                             'relativeCoverageNondiploid', 'calledLevel'
+                             ]
+    
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, column_names=self.column_names )
+        
+class CG_Gene( Tabular ):
+    file_ext = 'cg_gene'
+    def __init__(self, **kwd):
+        """Initialize CG_Gene datatype"""
+        Tabular.__init__( self, **kwd )
+        self.column_names = ['index', 'locus', 'allele', 'chromosome', 'begin', 'end',
+                             'varType', 'reference', 'call', 'xRef', 'geneId',
+                             'mrnaAcc', 'proteinAcc', 'symbol', 'orientation', 'component',
+                             'componentIndex', 'hasCodingRegion', 'impact', 'nucleotidePos',
+                             'proteinPos', 'annotationRefSequence', 'sampleSequence',
+                             'genomeRefSequence', 'pfam'
+                             ]
+   
+    def display_peek( self, dataset ):
+        """Returns formated html of peek"""
+        return Tabular.make_html_table( self, dataset, column_names=self.column_names )