Analyze_Reads() Function No Defined

[srdea93]

I was running this tool from the extraction step through the quantification step and I noticed that when trying to run arcasHLA quant, I received the following error:

arcasHLA quant --ref XXX -t 8 XXX.extracted.fq.gz Traceback (most recent call last): File "/rnd/users/sdea/software/arcasHLA/scripts/quant.py", line 162, in <module> num, avg, std = analyze_reads(args.file, paired, reads_file, False) NameError: name 'analyze_reads' is not defined

After looking into the source code to see if perhaps the function declaration was commented out, I noticed that it is seemingly not declared in quant.py nor in arcas_utilities.

[IoanFilip2]

Thank you for using our tool. The "quant" functionality of arcasHLA has not been documented entirely yet, and several bugs are currently being resolved as we are going through peer review with your publication. Please note that the analyze_reads function is currently defined in the align.py script. For single-end data, a bug currently appears to call this function prior to definition. This will be fixed in a subsequent update of arcasHLA-quant. Thanks!