Mercurial > repos > artbio > lumpy_sv
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
| author | artbio |
|---|---|
| date | Mon, 08 Jul 2024 22:23:10 +0000 |
| parents | 1ed8619a5611 |
| children |
line wrap: on
line diff
--- 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()