now using chunk mapper for tests

PhageTerm.py

@@ -48,7 +48,7 @@ from multiprocessing import Manager
 from _modules.utilities import checkPhageName
 from _modules.functions_PhageTerm import *
 from _modules.IData_handling import getAllReads,refData
-from _modules.GPU_mapper import gpuBasicMapper
+from _modules.GPU_chunkMapper import GPU_chunkMapper
 from _modules.common_readsCoverage_processing import processCovValuesForSeq
 from _modules.functions_PhageTerm_gpu import readsCoverageGPU
 
@@ -79,7 +79,7 @@ def main():
     if tParms.gpu!=0:
         RE,d_rinfo=getAllReads(inRawDArgs.fastq,fParms.seed,inRawDArgs.paired)
         ref_data = refData(inDArgs.refseq_liste, fParms.seed, inDArgs.hostseq)
-        mapper=gpuBasicMapper(RE,ref_data)
+        mapper=GPU_chunkMapper(RE,ref_data,"/pasteur/scratch/users/vlegrand/mapping_res",2)
         mapping_res=mapper.doMapping()
         exit()# TODO: remove this, this is to temporary in order to test the mapping of huge datasets on GPU.