Hi,

I am running the NAIBR to find structure variants.

Here is the error I get from the program.

Traceback (most recent call last):
File "NAIBR.py", line 6, in
from get_reads import *
File "src/get_reads.py", line 3, in
from utils import *
File "src/utils.py", line 1, in
from global_vars import *
File "src/global_vars.py", line 94, in
lmin,lmax = estimate_lmin_lmax()
File "src/global_vars.py", line 82, in estimate_lmin_lmax
dist = mate_pairs[read.query_name][0]-read.reference_end
TypeError: unsupported operand type(s) for -: 'int' and 'NoneType'

Here is the config file I used for the program:
#minimum mapping quality (default=40)
min_mapq=40

#input bam file
bam_file=../../scratch60/10X/longranger_alignment/10X2W82/possorted_bam.bam

#output directory (default=.)
outdir=10X2W82

#list of intervals not to be intcluded in analysis (default=None)
blacklist=None
#list in BEDPE format of novel adjacencies to be scored by NAIBR (default=None)
candidates=None
#maximum distance between read-pairs in a linked-read (default=10000)
d=10000

#minimum size of structural variant (default=lmax)
min_sv=1000

#number of cores (default=1)
cores=18

#minimum number of barcode overlaps supporting a candidate NA (default = 3)
k=3

Thanks.

Xing