Identical forward and reverse sequences for half of the reads in FASTQ files

[Accio]

Describe the bug In half of the pair-end reads in the FASTQ files, forward and reverse read sequences are identical. This is (correctly) not observed in the golden BAM file.

To Reproduce I created a github repo to describe the issue with a minimal reproducible example: https://github.com/Accio/NEAT-issue

Expected behavior Forward and reverse sequences in the FASTQ files should be distinct, and 100% mapped to the input genome.

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[joshfactorial]

I encourage you to visit our most up-to-date repo for this code: https://github.com/ncsa/NEAT - We have identified and fixed this bug. I may pull those changes back to this repo.