| Value | Meaning |
|---|---|
| scaffoldGaps | Only join gaps inside of scaffolds (marked by ns in FASTA). |
| scaffolds | Join gaps inside of scaffolds (marked by ns in FASTA) and try to join scaffolds. |
| contigs | Break input into contigs and re-scaffold everything; maintains scaffold gaps where new scaffolds are consistent. |
Determine which kinds of joins are allowed.