        **************************************************
        *                                                *
        *              2.10 SERIES NEWS                  *
        *                                                *
        **************************************************

SIGNIFICANT USER-VISIBLE CHANGES

    o coverage,AlignedRead-method has a changed interface (shift/width
    rather than start/end) and default behavior (return value in
    genome coordinates, rather than minimal covered region).

    o readAligned,character-method, type="Bowtie" and readFastq return
    FastqQuality by default.

    o coverage,AlignedRead-method now returns an RleList

NEW FEATURES

    o qa reports from _realign.txt, MAQMap files

    o QualityScoreDNAStringSet coercion methods

    o qa type="character" now accepts a filter argument with value
    srFilter()

    o alphabetByCycle supports variable-width XStringSets

    o qa,ShortReadQ and qa,list methods for qa on existing objects

BUG FIXES

    o Parse .gz realign files

    o alphabetScore,FastqQuality-method shifted quality by +1

        **************************************************
        *                                                *
        *              2.9 SERIES NEWS                   *
        *                                                *
        **************************************************

SIGNIFICANT USER-VISIBLE CHANGES

    o 454 quality scores are returned as FastqQuality-encoded

    o For functions accepting dirPath, pattern to name files, allow
    dirPath to be a vector of file names when pattern is character().

    o width() on ShortRead and derived classes (including AlignedRead
    now returns a vector of widths, of length equal to the length of
    the object.

NEW FEATURES

    o Add Bowtie as a 'type' value for qa and report

    o Add dustyScore() and dustyFilter() to identify low-complexity
    regions

    o Parse _qseq files (to ShortReadQ or XDataFrame)

    o Parse IPAR image intensity files _int.txt.p, _nse.txt.p, 
    _pos.txt

    o Create HTML-based quality assessment reports

    o Add trimLRPatterns() for ShortRead and derived classes
    (ShortReadQ, AlignedRead).

    o Add narrow() for ShortRead, QualityScore, and derived classes.

    o Use append() to append two objects of the same ShortReadQ or
    QualityScore and derived classes together

    o writeFastq for classes derived from ShortReadQ

    o Input functions support .gz or text files.

    o readIntensity reads Solexa image intensity files into R,
    including information about lane, tile, x, and y coordinates of
    each read.

    o readPrb returns different types of objects, depending on the
    'as' argument of the readPrb,character-method.

    o readXStringSet gets arguments skip, nrows; argument order
    changed slightly

    o New built-in SRFilters positionFilter, uniqueFilter to select
    reads aligning to particular positions, or to select only unique
    instances of reads aligning to each position.
    
    o readAligned gains a Solexa _results parser (_results files are
    listed as 'intermediate' in the Solexa manual, and not a good
    end-point for analysis)

    o readAligned gains a Bowtie output parser

    o readAligned gains ability to parse MAQ 0.7 version binary files

BUG FIXES

    o readQual would fail to read 454 quality scores correctly when
    these spanned more than one line of input per read

    o coverage treated reads as 1 base longer than they were

    o FastqQuality got the quality encoding off by one in as(x,
    "matrix")

    o qa_solexa.Rnw incorrectly displayed read occurences when lanes
    were presented out-of-order (an unusual occurence)

    o readAligned SolexaAlign, etc., updated to parse 'chromsome' and
    'position', and 'strand' information correctly

    o readAligned MAQMapview failed for most chromosome labels


        **************************************************
        *                                                *
        *              2.8 SERIES NEWS                   *
        *                                                *
        **************************************************

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)
