These classes provide the basic functionality to convert between data in external formats, such as sam, bed, or vcf, and data in internal formats.

In general external formats discard data critical for statistical analysis and cannot be converted directly into files usable by mapgd.

To perform these conversions we leverage the basic data-processing schema of mapgd, which requires that different

Thus

Sam files can be read by mapgd to make PRO files:

sam → PRO

GCF files can be used to write vcf files:

GCF → vcf

ped map tfam tped

PRO → MAP (MAP, PRO) → GCF (MAP, PRO) → LNK GCF → REL