formatting

stajichlab · Sep 17, 2019 · 6407dbb · 6407dbb
1 parent 9f42cc0
commit 6407dbb
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Showing 2 changed files with 2 additions and 4 deletions.
diff --git a/AAFTF/filter.py b/AAFTF/filter.py
@@ -152,7 +152,7 @@ def run(parser,args):
             cmd.extend(['in2=%s'%(revReads),'out2=%s_2.fastq.gz'%(clean_reads)])
 
         cmd.extend(['ref=%s'%(",".join(refmatch_bbduk))])
-
+        cmd.extend(['prealloc','qhdist=1'])
         printCMD(cmd)
         if args.debug:
             subprocess.run(cmd)

diff --git a/AAFTF/sourpurge.py b/AAFTF/sourpurge.py
@@ -72,9 +72,7 @@ def run(parser,args):
                    '--singleton', assembly_working]
     printCMD(sour_compute)
     subprocess.run(sour_compute, cwd=args.workdir, stderr=DEVNULL)
-
-    sour_classify = ['sourmash', 'lca', 'classify', '--db', SOUR,
-                     '--query', sour_sketch]
+    sour_classify = ['sourmash', 'lca', 'classify', '--db', SOUR,'--query', sour_sketch]
     printCMD(sour_classify)
     # output csv: ID,status,superkingdom,phylum,class,order,family,genus,species,strain
     Taxonomy = {}