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   numeric information on the coverage of reads across the region.

 * "region": A way of retrieving information about the reference
   sequence. Searching for features of type "region" will return a
   list of chromosomes or contigs in the reference sequence, rather
   than read alignments.

 * "chromosome": A synonym for "region".

B<Features> can be en masse in a single call, retrieved in a
memory-efficient streaming basis using an iterator, or interrogated
using a filehandle that return a series of SAM-format lines.

B<SAM alignment flags> can be retrieved using BioPerl's feature "tag"
mechanism. For example, to interrogate the FIRST_MATE flag, one
fetches the "FIRST_MATE" tag:

  warn "aye aye captain!" if $alignment->get_tag_values('FIRST_MATE');

The Bio::SeqFeatureI interface has been extended to retrieve all flags
as a compact human-readable string, and to return the CIGAR alignment