ERROR: LoadError: AssertionError: n_ref == contigs.count

[lautaro450]

Hello, I'm trying to compile AIControl (https://github.com/suinleelab/AIControl) That's using PureSeq.jl but I have a problem in julia 0.6.2:

ERROR: LoadError: AssertionError: n_ref == contigs.count
PureSeq.BamReader(::String, ::Symbol, ::PureSeq.ReferenceContigs) at /home/lautaro_arg/.julia/v0.6/PureSeq/src/BamReader.jl:27
#write_binned#7(::Bool, ::Function, ::String, ::Int64, ::Symbol) at /home/lautaro_arg/.julia/v0.6/PureSeq/src/BinnedReader.jl:29
(::PureSeq.#kw##write_binned)(::Array{Any,1}, ::PureSeq.#write_binned, ::String, ::Int64, ::Symbol) at ./:0
include_from_node1(::String) at ./loading.jl:576
include(::String) at ./sysimg.jl:14

I think may be is because Pure-seq was planned to use julia 0.5.2 but I can't use it because github not supported anymore tls 1.0 and 1.1 so when I tried to do a Pkg.add command in Julia 0.5.2 and the metadata started to download it I have a SSL error.

Exist some fix for this issue?

Thank you for the help!

[slundberg]

Did you ever talk with Nao and get this figured out? It seems like some mis alignment of reference contig counts, not sure if that would be effected by the version.

[hiranumn]

This may be caused because your input bam file is aligned to reference genome that is not hg38.
Would it possible to let me know what your reference is? I am guessing that it is hg19.

This is on my list of things to adjust.