LASTZ 1.02.11  Aug/21/2010  (not an official release)

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Fixed the cigarx field for --format=general, so that a run length of 1 is
omitted for indels.

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Fixed the behavior of --recoverseeds, which was failing to recover many HSPs
when seed denisty was high. This was due to left extension being blocked by
other seeds on that same hash-equivalent diagonal. Left extension is now
unblocked when --recoverseeds is enabled.

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Changed/corrected how the --segment option handles wildcard names when the
multiple action in used. To support this, the rewind command was added to the
segments file format.

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Sequence masking actions (softmask, xmask and nmask) are now allowed for the
multiple action.

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Command-line arguments beginning with two unicode non-breaking hyphens are now
recognized. Since these are used in some places within the README file, it is
natural for a user to copy them to the command line. Previously these were not
recognized, which led to a somewhat confusing error message.

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Fixed detection and reporting of improper gap penalties. Because the first base
in a gap is penalized as open+extend, open can be zero or negative as long as
that sum is strictly positive. Previously, a sum of zero was permitted, and a
negative sum was misleadingly reported as a problem with the open penalty. Now,
the sum must be strictly positive, and when it isn't the message more
accurately describes the problem.

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Fixed the implementation of --self with regard to mirror-image pairs.
Previously, alignments were internally restricted to be above the main diagonal
in the ungapped stage only. The mirrored twins were created prior to the gapped
stage, and the gapped stage operated on the full set of anchors. This had two
undesirable effects -- there was little computational savings, and the
resulting set of alignments could be assymetrical (due to small variations in
gap positioning). This behavior has been changed so that the above-diagonal
restriction occurs throughout the alignment process and mirrored twins are
created just prior to output.

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