From 8414d42d1bbcd0d877d7493a0ebfc4bc9f0a8d9f Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Mon, 30 Sep 2019 14:04:19 +0200
Subject: [PATCH] now using chunk mapper for tests
---
PhageTerm.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/PhageTerm.py b/PhageTerm.py
index 722b1bc..ee50ec1 100644
--- a/PhageTerm.py
+++ b/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.
--
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