attempt to fix bedtools compatability issue

photocyte · Jun 20, 2018 · 9f48d5f · 9f48d5f
1 parent 52cfe47
commit 9f48d5f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/omgene.py b/omgene.py
@@ -1098,7 +1098,7 @@ def prepareGeneregions(dict_seqInfo, dict_genomeInfo, path_wDir, int_numCores, i
 		path_allBaseLoci	= path_gDir + "/" + genomeId + ".bases"
 		path_mergedBaseLoci	= path_gDir + "/" + genomeId + ".bases.merged"
 		concatFiles(bases_tight, path_allBaseLoci)
-		callFunction("sort -k1,1V -k4,4n " + path_allBaseLoci + " | bedtools merge -s -i - > " + path_mergedBaseLoci)
+		callFunction("sort -k1,1V -k4,4n " + path_allBaseLoci + " | bedtools merge -s -c 4,5,6,7 -o distinct,distinct,distinct,distinct -i - > " + path_mergedBaseLoci)
 		sequences = [copy.deepcopy(a) for a in dict_seqInfo.values() if a["genome"] == path_genome]
 		for line in readCsv(path_mergedBaseLoci):
 			# Initialise the generegion in the holder dict