def MergeBamAlignment():
"""Run MergeBamAlignment"""
options.order("MergeBamAlignment", "picard_default")
unmapped_bam = options.get("UNMAPPED_BAM", options.prefix)
output = options.get("OUTPUT", get_prefix(unmapped_bam)[0] + ".bam")
ref = options.get("REFERENCE_SEQUENCE", options.index_loc.get(options.aligner).get(options.ref)[2])
opts = options.get("opts", "")
if not unmapped_bam is None:
opts += " OUTPUT=%s UNMAPPED_BAM=%s REFERENCE_SEQUENCE=%s" % (output, unmapped_bam, ref)
cl = [" ".join(["java -jar", options.get("javamem"), path(options.get("picard_home")) / "MergeBamAlignment.jar", opts])]
run_cmd(cl, unmapped_bam, output, options.get("run"), msg="Running MergeBamAlignment")
else:
print >> sys.stderr, "required argument unmapped_bam missing"
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"
