In this release we modified the output of delta2vcf to be fully compliant with vcf4.2 specification, validated by vcf-validator from vcftools. We also rolled back some changes in mummerplot and removed extra gnuplot options that may be incompatible with gnuplot version 4 or 5. We performed additional validation of the nucmer output.
Known issues:
- use of the --maxmatch option results in memory overflow on certain reference sequences that contain long stretches of homopolymers; we are still investigating this issue. For now please use --batch 1 instead of --maxmatch, if --maxmatch fails, this will use seeds that may repeat between different reference sequences, but not within the same input sequence.