--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/VarscanHit_v2_2_8.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,176 @@
+# 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.checker.CheckerException import CheckerException
+from commons.core.parsing.VarscanHit import VarscanHit
+
+class VarscanHit_v2_2_8(VarscanHit):
+    
+    def __init__(self, chrom = "", position = "", ref = "", cns = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = "", mapQualRef = "", mapQualVar = "", readsRefPlus = "", readsRefMinus = "", readsVarPlus = "", readsVarMinus = "", var = ""):
+        self._cns = cns
+        self._mapQualRef = mapQualRef
+        self._mapQualVar = mapQualVar
+        self._readsRefPlus = readsRefPlus
+        self._readsRefMinus = readsRefMinus
+        self._readsVarPlus = readsVarPlus
+        self._readsVarMinus = readsVarMinus
+        VarscanHit.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue)
+        
+    ## Equal operator
+    #
+    # @param o a VarscanFileAnalysis instance
+    #    
+    def __eq__(self, o):
+        if self._cns == o._cns:
+            return VarscanHit.__eq__(self, o)
+        return False
+    
+    def setCns(self, consensus):
+        self._cns = consensus
+        
+    def setMapQualRef(self, mapQualRef):
+        self._mapQualRef = mapQualRef
+        
+    def setMapQualVar(self, mapQualVar):
+        self._mapQualVar = mapQualVar
+        
+    def setReadsRefPlus(self, readsRefPlus):
+        self._readsRefPlus = readsRefPlus
+        
+    def setReadsRefMinus(self, readsRefMinus):
+        self._readsRefMinus = readsRefMinus
+        
+    def setReadsVarPlus(self, readsVarPlus):
+        self._readsVarPlus = readsVarPlus
+        
+    def setReadsVarMinus(self, readsVarMinus):
+        self._readsVarMinus = readsVarMinus
+    
+    def getCns(self):
+        return self._cns
+        
+    def getMapQualRef(self):
+        return self._mapQualRef
+        
+    def getMapQualVar(self):
+        return self._mapQualVar
+        
+    def getReadsRefPlus(self):
+        return self._readsRefPlus
+        
+    def getReadsRefMinus(self):
+        return self._readsRefMinus
+        
+    def getReadsVarPlus(self):
+        return self._readsVarPlus
+        
+    def getReadsVarMinus(self):
+        return self._readsVarMinus
+    
+    def getHeader(self):
+        return "Chrom\tPosition\tRef\tCons\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tMapQual1\tMapQual2\tReads1Plus\tReads1Minus\tReads2Plus\tReads2Minus\tVarAllele\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\t%s\t%s\t%s\t%s\t%s\t%s\n" % (self.getChrom(), self.getPosition(), self.getRef(), self.getCns(), self.getReadsRef(), self.getReadsVar(), self.getVarFreq(), self.getStrandsRef(), self.getStrandsVar(),  self.getQualRef(), self.getQualVar(), self.getPValue(), self.getMapQualRef(), self.getMapQualVar(), self.getReadsRefPlus(), self.getReadsRefMinus(), self.getReadsVarPlus(), self.getReadsVarMinus(), self.getVar())
+    
+    def setAttributes(self, lResults, iCurrentLineNumber):
+        if lResults[0] != '':
+            self.setChrom(lResults[0])
+        else:
+            raise CheckerException ("The field Chrom is empty in varscan file in line %s" % iCurrentLineNumber)
+        if lResults[1] != '':
+            self.setPosition(lResults[1])
+        else:
+            raise CheckerException ("The field Position is empty in varscan file in line %s" % iCurrentLineNumber)
+        if lResults[2] != '':
+            self.setRef(lResults[2])
+        else:
+            raise CheckerException ("The field Ref is empty in varscan file in line %s" % iCurrentLineNumber)
+        if lResults[3] != '':
+            self.setCns(lResults[3])
+        else:
+            raise CheckerException ("The field Cons is empty in varscan file in line %s" % iCurrentLineNumber)
+        if lResults[4] != '':
+            self.setReadsRef(lResults[4])
+        if lResults[5] != '':
+            self.setReadsVar(lResults[5])
+        if lResults[6] != '':
+            self.setVarFreq(lResults[6])
+        if lResults[7] != '':
+            self.setStrandsRef(lResults[7])
+        if lResults[8] != '':
+            self.setStrandsVar(lResults[8])
+        if lResults[9] != '':
+            self.setQualRef(lResults[9])
+        if lResults[10] != '':
+            self.setQualVar(lResults[10])
+        if lResults[11] != '':
+            self.setPValue(lResults[11])
+        if lResults[12] != '':
+            self.setMapQualRef(lResults[12])
+        if lResults[13] != '':
+            self.setMapQualVar(lResults[13])
+        if lResults[14] != '':
+            self.setReadsRefPlus(lResults[14])
+        if lResults[15] != '':
+            self.setReadsRefMinus(lResults[15])
+        if lResults[16] != '':
+            self.setReadsVarPlus(lResults[16])
+        if lResults[17] != '':
+            self.setReadsVarMinus(lResults[17])
+        if lResults[18] != '':
+            self.setVar(lResults[18])
+        else:
+            raise CheckerException ("The field varAllele is empty in varscan file in line %s" % iCurrentLineNumber)
+            
+    def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
+        varscanString = varscanString.rstrip()
+        lvarscanStringItem = varscanString.split(fieldSeparator)
+        if len(lvarscanStringItem) < 19:
+            raise CheckerException ("This varscan line (l.%s) is not complete" % iCurrentLineNumber)
+        self.setAttributes(lvarscanStringItem, iCurrentLineNumber)
+        
+    def convertVarscanHit_v2_2_8_To_VarscanHit(self):
+        iVarscanHit = VarscanHit()
+        iVarscanHit.setChrom(self.getChrom())
+        iVarscanHit.setPosition(self.getPosition())
+        iVarscanHit.setRef(self.getRef())
+        iVarscanHit.setVar(self.getVar())
+        iVarscanHit.setReadsRef(self.getReadsRef())
+        iVarscanHit.setReadsVar(self.getReadsVar())
+        iVarscanHit.setVarFreq(self.getVarFreq())
+        iVarscanHit.setStrandsRef(self.getStrandsRef())
+        iVarscanHit.setStrandsVar(self.getStrandsVar())
+        iVarscanHit.setQualRef(self.getQualRef())
+        iVarscanHit.setQualVar(self.getQualVar())
+        iVarscanHit.setPValue(self.getPValue())
+        return iVarscanHit
+        
\ No newline at end of file