Unintended default scoring in versions before 1.01.00

[rsharris]

Default scoring in early versions was inadvertently set to scores used in early prototypes of the tool.

The default has been changed to something more reasonable, though it still has not undergone serious test. On the off chance that users want to reproduce results from that earlier default, the unadvertised option --scoring=1.00.XX has been added.

It is highly recommended that users explicitly set their scoring option. (Use --help=scoring to see choices). For example, if you have Oxford Nanopore reads the pre-canned scores for PacBio will not produce the best results. The two technologies have different sequencing error profiles. The difference is most evident in indels, as one technology skews to insertions, the other to deletions. The pre-canned scores reflect those profiles.