Reove Gap Extension penality parameter in bwa

Author: ljq12697

Choruslib/bwa.py

@@ -172,7 +172,7 @@ def bwaalign(bwabin, reffile, inputfile, outfile, threadnumber=1):
     inputfile = subprocesspath.subprocesspath(inputfile)
     outfile = subprocesspath.subprocesspath(outfile)
 
-    bwacmd = ' '.join([bwabin, 'mem', '-O',' 0',' -B',' 0',' -E',' 0',' -k',' 5', '-t',str(threadnumber), reffile, inputfile, '>', outfile])
+    bwacmd = ' '.join([bwabin, 'mem', '-O',' 0',' -B',' 0',' -k',' 5', '-t',str(threadnumber), reffile, inputfile, '>', outfile])
 
     print(bwacmd)
 
@@ -278,7 +278,7 @@ def bwaloci(bwabin, reffile, inputfile, threadnumber=1):
     inputfile = subprocesspath.subprocesspath(inputfile)
 
 
-    bwacmd = ' '.join([bwabin, 'mem', '-O',' 0',' -B',' 0',' -E',' 0',' -k',' 5', '-t',str(threadnumber), reffile, inputfile])
+    bwacmd = ' '.join([bwabin, 'mem', '-O',' 0',' -B',' 0',' -k',' 5', '-t',str(threadnumber), reffile, inputfile])
 
     print(bwacmd)
 
@@ -315,7 +315,7 @@ def bwafilter(bwabin, reffile, inputfile, minas, maxxs ,threadnumber=1 ):
 
     inputfile = subprocesspath.subprocesspath(inputfile)
 
-    bwacmd = ' '.join([bwabin, 'mem', '-O',' 0',' -B',' 0',' -E',' 0',' -k',' 5', '-t',str(threadnumber), reffile, inputfile])
+    bwacmd = ' '.join([bwabin, 'mem', '-O',' 0',' -B',' 0',' -k',' 5', '-t',str(threadnumber), reffile, inputfile])
 
     print(bwacmd)
 
@@ -441,4 +441,4 @@ def bwareflength(bwabin, reffile):
     # res = bwaloci(bwapath, '../Test/Testsampe/DM_404.fa', '../Test/Testsampe/DM_test.faprobes.fa',threadnumber=4)
     #
     # for i in res:
-    #     print(i)
+    #     print(i)