Simplify set of sequences used for unit tests

In addition to removing some sequences that we weren't really using,
this commit adds sequences that don't align perfectly with the
reference.
Add imperfect alignments to unit test cases
Implement fastq input
Include SAM header in output
New function rapi_reads_clear
Wrap and test rapi_reads_clear
Introduce rapi_ssize_t type
Turn "capacity" into a synthesized read-only attribute
Bugfix on bounds checking and IndexError
Whitespace
Work in batches