In essence, cas format files contain data about the relationships between sequences in other files.
In particular, cas files contain the following information:
- General info such as: program that made the file, its version and its parameters.
- The file names for the reference sequences.
- The file names for the read sequences.
- Information about the reference sequences: their number, lengths, etc.
- The scoring scheme used when making the file.
- Information about each read:
- Whether it matches anywhere.
- Which reference sequence does it match to.
- Alignment between the reference sequence and the read.
- The number of places the read matches.
- Whether the read is part of a pair.