diff extractSplitReads_BwaMem.py @ 6:48e97429a749 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit 37c0f0938a5cad74c954a89827a6a08bbbb81cb0

--- a/extractSplitReads_BwaMem.py	Sun May 24 18:48:46 2020 -0400
+++ b/extractSplitReads_BwaMem.py	Mon Jul 08 22:23:10 2024 +0000
@@ -21,7 +21,7 @@
             continue
         for el in sam.tags:
             if "SA:" in el:
-                if(len(el.split(";"))) <= numSplits:
+                if (len(el.split(";"))) <= numSplits:
                     split = 1
                     mate = el.split(",")
                     mateCigar = mate[3]
@@ -103,7 +103,6 @@
         cigarOps = []
         for opString in cigarOpStrings:
             cigarOpList = atomicCigarSearch.findall(opString)
-#            print cigarOpList
             # "struct" for the op and it's length
             cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1])
             # add to the list of cigarOps
@@ -120,8 +119,7 @@
             cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1])
             # add to the list of cigarOps
             cigarOps.append(cigar)
-#            cigarOps = cigarOps
-    return(cigarOps)
+    return cigarOps
 
 
 def calcQueryPosFromCigar(cigarOps):
@@ -202,7 +200,8 @@
                       help='''Include alignments marked as duplicates.
                       Default=False''')
     parser.add_option("-m", "--minNonOverlap", dest="minNonOverlap",
-                      default=20, type="int", help='''minimum non-overlap between
+                      default=20, type="int",
+                      help='''minimum non-overlap between
                       split alignments on the query (default=20)''',
                       metavar="INT")
     (opts, args) = parser.parse_args()