SAM Alignment Section
A few remarks on the exported alignment section:
- Unmapped reads are not exported.
- If pairs are not on the same contig, the mates will be exported as single reads.
- Multi segment mappings will be imported as a paired data set.
- If the reference name contains spaces, these are removed. Each occurrence of '=' (equals sign) and '@' (at sign) in the reference name is replaced by an '_' (underscore).
- The exported CIGAR string uses 'M' to indicate match or mismatch and does not use '=' (equals sign) or 'X'.