Using bam alignment

[arichards2564]

STAR-SEQR/starseqr.py

Lines 443 to 446 in 8889bc8

	elif args.star_bam:
	chimflag = 2048
	star_bam_local = new_prefix + ".Chimeric.out.bam"
	su.common.sam_2_coord_bam(new_prefix + ".Chimeric.out.sam", star_bam_local, args.threads)

I'm trying to use a pre-aligned bam and it errors here because it looks for sam file that doesn't exist. I believe this is a mistake. Do I need to have both the sam and bam file available?