        **************************************************
        *                                                *
        *              2.8 SERIES NEWS                   *
        *                                                *
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SIGNIFICANT USER-VISIBLE CHANGES

    o SRFilter allows construction of filters that can be used to
    subset existing data objects, or filter incoming (readAligned, at
    the moment) objects.

    o readAligned for Solexa-based alignments return 'strand'
    information as factor with levels "-", "+", "*" (strand not
    relevant), NA (no strand information available).

    o srorder, srsort, srrank, and srduplicated for AligendRead class
    now sort based on chromosome, strand, position AND sread; previous
    behavior can be recovers by extracting the sequences
    srsort(sread(aln)), etc.

    o Functions using SolexaPath now search all relevant directories,
    e.g., in analysisPath, rather than the first

NEW FEATURES


BUG FIXES

    o 'run' in eland_export files is correctly parsed as a factor

(start date: 29 September, 2008)
