9a9778a6d9f4b2751a7ff5e0a2d4dcd7e6eee0a2,rnaseq/src/run_STAR.py,,,#,20

Before Change

args = parser.parse_args()

if args.fastq1.endswith(".gz"):
    with gzip.open(args.fastq1) as f:
        f.readline()
        seq = f.readline().strip()
        read_length = len(seq)
else:
    with open(args.fastq1) as f:
        f.readline()
        seq = f.readline().strip()
        read_length = len(seq)
overhang = read_length-1

if read_length<=201:
    starcmd="STAR"

After Change

parser.add_argument("--outSAMattributes", default=["NH", "HI", "AS", "nM", "NM", "ch"], nargs="+")
parser.add_argument("--chimSegmentMin", default="15", help="Minimum chimeric segment length; switches on detection of chimeric (fusion) alignments")
parser.add_argument("--chimJunctionOverhangMin", default="15", help="Minimum overhang for a chimeric junction")
parser.add_argument("--chimOutType", default=["WithinBAM", "SoftClip"], nargs="+", help="")
parser.add_argument("--chimMainSegmentMultNmax", default="1", help="")
parser.add_argument("--genomeLoad", default="NoSharedMemory")
parser.add_argument("--STARlong", action="store_true", help="Use STARlong instead of STAR")
parser.add_argument("-t", "--threads", default="4", help="Number of threads")
args = parser.parse_args()

if args.STARlong:

Instances