A number of bugs were fixed to improve performance and make the pipeline compatible with more Linux environments.
-- FASTQ commandline tools were updated for compatibility with Python 3+.
-- Bedgraphs are stored in numpy arrays for improved memory efficiency in larger genomes.
-- Added arguments --gtf_gene_tag and --gtf_transcript_tag in nanoPARE_setup.sh for more options in parsing GTF annotations.
-- Improved parsing of annotations in the GFF3 format.
-- Fixed a bug where empty lines in a FASTQ file resulted in a crash.