--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/VarscanHit_WithTag.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,70 @@
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+
+
+from commons.core.parsing.VarscanHit import VarscanHit
+
+class VarscanHit_WithTag(VarscanHit):
+    
+    def __init__(self, tag = "", chrom = "", position = "", ref = "", var = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = ""):
+        self._tag = tag
+        VarscanHit.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue)
+        
+    def __eq__(self, o):
+        if self._tag == o._tag: 
+            return VarscanHit.__eq__(self, o)
+        return False
+    
+    def setTag(self, tag):
+        self._tag = tag
+        
+    def getTag(self):
+        return self._tag
+    
+    def getHeader(self):
+        return "Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tTag\n"
+    
+    def getVarscanLine(self):
+        return "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (self.getChrom(), self.getPosition(), self.getRef(), self.getVar(), self.getReadsRef(), self.getReadsVar(), self.getVarFreq(), self.getStrandsRef(), self.getStrandsVar(),  self.getQualRef(), self.getQualVar(), self.getPValue(), self.getTag())
+    
+    def setAttributes(self, lResults, iCurrentLineNumber):
+        VarscanHit.setAttributes(self, lResults, iCurrentLineNumber)
+        if lResults[12] != '':
+            self.setTag(lResults[12])
+            
+    def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
+        varscanString = varscanString.rstrip()
+        lvarscanStringItem = varscanString.split(fieldSeparator)
+        if len(lvarscanStringItem)<13:
+            for i in range(len(lvarscanStringItem), 13):
+                lvarscanStringItem.append ("")
+        self.setAttributes(lvarscanStringItem, iCurrentLineNumber)
+    
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