Attribute Error: BamScanner has no attribute 'indel_table'.

[maheetha]

Hello!

My name is Maheetha, and I'm a student at a lab at Stanford trying to use WASP for allele-specific expression purposes.

I have a couple of bugs that I was hoping you might have the answer for. I have everything set up as according to the README file and have all of the SNPs separated by chromosome in a separate directory.

When I run find_intersecting_snps.py, it finishes chr1, chr10, and chr11 sucessfully. During chr11, it doesn't say that it "skips any SNPs", but it skipped SNPs for chr1 and chr10.

However, I think the bigger issues is that it finishes after chr11 and doesn't do chr12 or any other chromosome for that matter.

When I try to do chr8 by itself or start from chr12 (so I remove chr1, chr10, and chr11 from the snp directory) it gives me this error:

Traceback (most recent call last):
File "./WASP_master/mapping/find_intersecting_snps.py", line 810, in
is_sorted=options.is_sorted)
File "./WASP_master/mapping/find_intersecting_snps.py", line 764, in main
remap_num_name, fastq_names, snp_dir)
File "./WASP_master/mapping/find_intersecting_snps.py", line 259, in init
self.switch_chr()
File "./WASP_master/mapping/find_intersecting_snps.py", line 320, in switch_chr self.skip_chr()
File "./WASP_master/mapping/find_intersecting_snps.py", line 413, in skip_chr self.empty_table()
File "./WASP_master/mapping/find_intersecting_snps.py", line 686, in empty_table
self.empty_slot_paired()
File "./WASP_master/mapping/find_intersecting_snps.py", line 522, in empty_slot_paired
self.shift_SNP_table()
File "./WASP_master/mapping/find_intersecting_snps.py", line 649, in shift_SNP_table
for indel_pos in self.indel_table[cur_slot]:
AttributeError: BamScanner instance has no attribute 'indel_table'

I don't have any indels in any of my chromosome SNP files, and I'm not sure why suddenly after chr11, it's throwing me this error. I'm not really able to spot the issue.

I was wondering if you had some ideas.

Thank you so much for your help,

Best,

Maheetha