Bamutils count question

[mbreese]

Sorry for the late reply...

Try to update your code that you are using (git pull, if you used git). This bug ended up catching me too, and I wrote the thing... it should be fixed in the repository.

[arcys]

hi,

I am a newbie in using command-line tools for NGS. Just tried to use the bamutils from NGSUtils in processing the bam file from the core. I tried to calculate the RPKM and reads by using the following command:

./bamutils count gtf hg19_genes.gtf Tophat.bam

It runs for a few minutes and returns the following message:
Reading GTF file...
GTF file missing isoform annotation! Each transcript will be treated separately.
Done! (0:28)
1.6% - 0:12 [> ] ETA: 11:33 | FUCA1Traceback (most recent call last):
File "/root/ngsutils/bam_utils/bam_count.py", line 222, in <module>
modelobj.count(bamfile, stranded, coverage, uniq_only, rpkm, norm, multiple, whitelist, blacklist)
File "/root/ngsutils/bam_utils/count/count.py", line 52, in count
count, reads = _fetch_reads(bam, chrom, strand if stranded else None, starts, ends, multiple, False, whitelist, blacklist, uniq_only)
TypeError: 'int' object is not iterable

So how can I fix it? THX!