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vgl-hub / gfastats

A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

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Agp integration does not support terminal gaps

gf777 opened this issue · comments

commented

The presence of a terminal gap (gap at the end of scaffolds, e.g. attached file between scaffold25 and 28) will result in incorrect behavior
hap.unlocs.no_hapdups.agp.zip

commented

This issue has been fixed in the latest commit. Terminal gaps in AGP (both at the beginning and end of sequences) are now ignored and a warning about their presence in the AGP is issued. This is consistent with the requirement of avoiding terminal gaps at scaffold ends (e.g. in NCBI submissions).