def FastqToSam():
"""Write unaligned bam file"""
options.order("FastqToSam", "picard_default")
f1 = options.get("FASTQ", current_prefix(options.read_suffix + options.ext_fq))
f2 = options.get("FASTQ2",read2())
qv = options.get("QUALITY_FORMAT", "Standard")
output = options.get("OUTPUT", None)
sample_name = options.get("SAMPLE_NAME", get_prefix(f1)[0])
opts = options.get("opts", "")
if not output is None and not sample_name is None:
opts += " FASTQ=%s FASTQ2=%s QUALITY_FORMAT=%s SAMPLE_NAME=%s OUTPUT=%s" % (f1, f2, qv, sample_name, output)
cl = [" ".join(["java -jar", options.get("javamem"), path(options.get("picard_home")) / "FastqToSam.jar", opts])]
run_cmd(cl, f1, output, options.get("run"), msg="Running FastqToSam")
else:
print >> sys.stderr, "required argument missing"
def read2():
"""Return read 2 if paired end"""
retval = "none"
if options.paired_end:
retval = current_prefix(options.read2_suffix + options.ext_fq)
return retval
