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and in Slice to make more consistant.

in get_repeatmasked_seq and _mask_features methods

overload get_repeatmasked_seq method, and _mask_feature as consequence to allow soft masking (replace repeat by their lower case equivalent, needed for blastz for example). BTW, fixed little bug, previously when a repeat was overlapping slice, but was partly out of range, no masking was done with it. Now it does.

In _parse_features, making better use of strandedness information to make sure query and hit start and end coordinates are turned the right way around.

Removed deprecated Repeat, RepeatI modules
Added a few more PODs

use a consensus from the database if one exists

Removed contig_list definition from clone constructor. Ctgs were not retrieved if list was defined

Sped up general feature creation a bit more

was assuming a straight array.

Superfamily SeqFeatures were created with analysis=>analysisid instead of analysis=>analysis, which made SeqFeature choke.  Fix0red.