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    Minutes libSlice Meeting (04/02/03)

    April 2, 2003 at 3:30 in Conference Room B

    Miguel Covarrubias, Art Delcher, Pawel Gajer, Michael Holmes, Mihai Pop, Steven Salzberg, Michael Schatz, and Martin Shumway attended.

    libSlice Issues

    1. As an ad-hoc rule, clients of libSlice will set the quality value of a gap in a read to be the minimum quality value of the two flanking elements in the read. This value will be written directly into the slice before it is provided to libSlice, because libSlice operates on a single slice at a time and may not have the flanking information available. If the client leaves the quality value at 0, libSlice will continue the current practice and assign a quality value of 20 to the gap. libSlice will use the gap quality values in consensus calling, ambiguity code calculations, and consensus quality value calculations.

    2. In the absense of a rigourous model for diploid alignments, libSlice will continue to utilize the model in which only one outcome is possible as the consensus of a slice. Under this model, the consensus quality value of an ambiguous slice will be a measure of the confidence that the most likely base is the true consensus of the slice. A model for diploid alignments will be investigated and implemented as needed.

    3. Cloe will mark edited bases with a quality value of 40 instead of 99. This will remove the overwhelming bias towards edited bases when calling the consensus by libSlice. Cloe should allow for this value to be set as a global policy.

    4. libSlice will continue to support dual modes of operation in which both ambiguity codes and non-ambiguous bases can be called as the consensus of a slice, as based on the parameters set by the client. SliceService will allow for this parameter to be set by an option element in the Slice XML DTD.

    5. libSlice will continue to output IUPAC ambiguity codes when requested and not the extended ambiguity codes defined by Churchill and Waterman. libSlice will continue to support tests for each of the 5 possibilities in the ambiguity code for a slice, so that a client can determine if '-' should have be included in the ambiguity code.

    Global Issues

    1. ca2ta will recall the consensus prior to uploading so that the view of the data in the database will be consistent with the needs of Cloe. An option will be provided to specify if ambiguity codes or non-ambiguous bases should be called as the consensus.

    2. TIGR Editor and TIGR Assembler will be retired on June 1. Quality classes will be removed from the database and get_quality_class.spl will be replaced.


    $Date: 2005/07/29 02:55:17 $