svr_inconsistent_sets

Separate out inconsistent sets

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Example:

    svr_inconsistent_sets < pg.sets 2> inconsistent.pg.sets > consistent.pg.sets
or
    svr_inconsistent_sets -s -f assignments < pg.sets 2> inconsistent.pg.sets > consistent.pg.sets

would write consistent sets to consistent.pg.sets and inconsistent sets to inconsistent.pg.sets. The second form will

    1. strip comments before the comparison
    2. write proposed assignments to the file "assignments".

Using the second form, the consistent.pg.sets include sets corrected by the proposed assignments.

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Command-Line Options

-f proposed.assignments

This causes correction of the assignments that can trivially be fixed. The resulting proposed set of assignments gets written to the designated file.

-s [strip comments]

This causes comments to be stripped from functions before the comparisons.

-k [update assignments using kmers - a performance hit]

Output Format

Consistent sets are written to STDOUT, while inconsistent sets get writeen to STDERR.