r-bioc-genomicalignments 1.14.1-1 / usr / lib / R / site-library / GenomicAlignments / NEWS

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CHANGES IN VERSION 1.14.0
-------------------------

SIGNIFICANT USER-LEVEL CHANGES

    o makeGAlignmentPairs() no more drops pairs with discordant seqnames.

    o Change 'maxgap' and 'minoverlap' argument defaults in methods of the
      findOverlaps() so they adhere to the new argument defaults of the generic
      defined in IRanges 2.12.0. See NEWS file in the IRanges package for more
      information about this change.

DEPRECATED AND DEFUNCT

    o Remove 'force' argument from seqinfo() and seqlevels() setters (the
      argument got deprecated in BioC 3.5 in favor of new and more flexible
      'pruning.mode' argument).

BUG FIXES

    o Fix bug in pairing code of readGAlignmentPairs() when one mate in a pair
      is lost because of user-supplied filtering (e.g. mapqFilter=10).


CHANGES IN VERSION 1.12.0
-------------------------

NEW FEATURES

    o seqlevels() setter now supports "fine" and "tidy" pruning modes on
      GAlignmentsList objects (in addition to "coarse" mode, which is the
      default).

    o Add "pcompare", "is.unsorted", "order", "sort", and "rank" methods for
      GAlignments objects.

    o Add encodingHalves(), a low-level overlap encoding utility.

SIGNIFICANT USER-LEVEL CHANGES

    o Tweak behavior of isCompatibleWithSplicing() on paired-end encodings.

    o Minor tweaks to low-level encoding utilities Lencoding(), Rencoding(),
      Lnjunc(), Rnjunc(), and njunc(). All of them now are based on new
      encodingHalves() low level utility.

    o Speed up first() and last() on GAlignmentPairs object when the object has
      no names. Thanks to Pete Hickey for the suggestion.

    o 2x to 3x speedup to "junctions" methods.

DEPRECATED AND DEFUNCT

    o Argument 'force' of seqinfo() and seqlevels() setters is deprecated in
      favor of new and more flexible 'pruning.mode' argument.

BUG FIXES

    o Make grglist() work on GAlignmentPairs object with strandMode set to 0.
      Thanks to Dario Strbenac for catching and reporting this.

    o Fix bug affecting extractSteppedExonRanks() on certain paired-end
      encodings.

    o Fix subsetting of OverlapEncodings objects and modernize their "show"
      method.


CHANGES IN VERSION 1.10.0
-------------------------

NEW FEATURES

    o The GAlignmentPairs container now supports pairs with discordant strand
      and/or seqnames. The "granges" and "ranges" methods for GAlignmentPairs
      objects get new argument 'on.discordant.seqnames' to let the user control
      how to handle pairs with discordant seqnames.
      See ?GAlignmentPairs for more information.

    o Add "invertStrand" method for GAlignmentPairs objects.

    o Add 'use.names' argument to the "ranges", "granges", "grglist" and
      "rglist" methods for GAlignments and GAlignmentsList objects.

    o Add 'use.names' argument to the "granges" and "grglist" methods for
      GAlignmentPairs objects.

    o Add "ranges" method for GAlignmentPairs objects.

SIGNIFICANT USER-LEVEL CHANGES

    o The 'at' argument of pileLettersAt() is now expected to be a GPos object
      (GRanges still accepted).

    o 50x speed-up of the granges() extractor for GAlignmentPairs object. The
      improvement is based on a suggestion by Arne Muller. 

DEPRECATED AND DEFUNCT

    o Remove left() and right() generics and methods (were defunct in BioC 3.3).

    o Remove 'invert.strand' argument from "first" and "last" methods for
      GAlignmentPairs objects (was defunct in BioC 3.3).

    o Remove strand() setter for GAlignmentPairs objects (was defunct in BioC
      3.3).

    o Remove 'order.as.in.query' argument from "grglist" method for
      GAlignmentPairs objects and from "grglist" and "rglist" methods for
      GAlignmentsList objects (was defunct in BioC 3.3).

BUG FIXES

    o Fix 'use.names=FALSE' in "grglist" and "rglist" methods for
      GAlignmentsList objects.


CHANGES IN VERSION 1.8.0
------------------------

NEW FEATURES

    o Add coercion from GAlignments or GAlignmentPairs to DataFrame, and from
      GAlignmentsList to GAlignmentPairs.

SIGNIFICANT USER-LEVEL CHANGES

    o Use DESeq2 instead of DESeq in summarizeOverlaps examples (better late
      than never).

DEPRECATED AND DEFUNCT

    o After being deprecated in BioC 3.2, the left() and right() getters and
      strand() setter for GAlignmentPairs objects are now defunct.

    o After being deprecated in BioC 3.2, the 'invert.strand' argument of the
      first() and last() getters for GAlignmentPairs objects are now defunct.

    o After being deprecated in BioC 3.2, the 'order.as.in.query' argument of
      the "grglist" method for GAlignmentPairs objects is now defunct.

    o After being deprecated in BioC 3.2, the 'order.as.in.query' argument of
      the "rglist" and "grglist" methods for GAlignmentsList objects are now
      defunct.

    o Remove the "mapCoords" and "pmapCoords" methods (were defunct in BioC
      3.2).

    o Remove the readGAlignment*FromBam() functions (were defunct in BioC 3.2).

BUG FIXES

    o seqnames() setter for GAlignments objects is now consistent with
      seqnames() setter for GRanges objects.


CHANGES IN VERSION 1.6.0
------------------------

NEW FEATURES

    o Add strandMode() getter and setter for GAlignmentPairs objects in
      response to the following post:

        https://support.bioconductor.org/p/65844/

      See ?strandMode for more information.

    o The readGAlignment*() functions now allow repeated seqnames in the BAM
      header.

    o Add "coverage" method for GAlignmentsList objects.

    o The strand setter now works on a GAlignmentsList object in a restricted
      way (only strand(x) <- "+" or "-" or "*" is supported).

SIGNIFICANT USER-LEVEL CHANGES

    o summarizeOverlaps() now returns a RangedSummarizedExperiment object
      (defined in the new SummarizedExperiment package) instead of an "old"
      SummarizedExperiment object (defined in the GenomicRanges package).

    o Slightly modify the behavior of junctions() on a GAlignmentPairs object
      so that the returned ranges now have the "real strand" set on them.
      See ?junctions and the documentation of the 'real.strand' argument in
      the man page of GAlignmentPairs objects for more information.

    o Add 'real.strand' argument to first() and last() getters for
      GAlignmentPairs objects.

DEPRECATED AND DEFUNCT

    o Deprecate left() and right() getters and strand() setter for
      GAlignmentPairs objects.

    o Deprecate 'invert.strand' argument of first() and last() getters for
      GAlignmentPairs objects.

    o Deprecate 'order.as.in.query' argument of "grglist" method for
      GAlignmentPairs objects.

    o Deprecate 'order.as.in.query' argument in "rglist" method for
      GAlignmentsList objects (this concept is not defined for these objects
      in general and the argument was ignored anyway).

    o After being deprecated in BioC 3.1, the "mapCoords" and "pmapCoords"
      methods are now defunct. mapToAlignments() should be used instead.

    o After being deprecated in BioC 3.1, the readGAlignment*FromBam()
      functions are now defunct. Everybody says "Let's all use the
      readGAlignment*() functions instead! (no FromBam suffix). Yeah!"

BUG FIXES

    o Various fixes to grglist/granges/rglist/ranges methods for
      GAlignmentsList objects:
      - Respect cigar information (as claimed in man page).
      - Restore 'drop.D.ranges' argument in "grglist" method (mistakenly got
        deprecated at the beginning of BioC 3.2 devel cycle).
      - The 'drop.D.ranges' argument in "rglist" method now works (was
        ignored).
      - Handle empty list elements.


CHANGES IN VERSION 1.4.0
------------------------

NEW FEATURES

    o All "findOverlaps" methods now support 'select' equal "last" or
      "arbitrary" (in addition to "all" and "first").

SIGNIFICANT USER-LEVEL CHANGES

    o Add mapToAlignments(), pmapToAlignments(), mapFromAlignments(), and
      pmapFromAlignments() as replacements for the "mapCoords" and "pmapCoords"
      methods for GAlignments objects.

    o Clarify use of 'fragments' in summarizeOverlaps() man page.

    o Tweak "show" method for GAlignments objects to display a shorter
      version of long CIGARs.

    o Add checks and more helpful error message for summarizeOverlaps() when
      "file does not exist"

DEPRECATED AND DEFUNCT

    o Deprecated readGAlignment*FromBam() functions in favor of 
      readGAlignments(), readGAlignmentPairs(), readGAlignmentsList() and
      readGappedReads().

    o Deprecated "mapCoords" and "pmapCoords" methods.

    o Removed Lngap(), Rngap(), introns(), and
      makeGAlignmentsListFromFeatureFragments() functions, and "ngap", "map",
      "pmap", and "splitAsListReturnedClass" methods (were defunct in
      GenomicAlignments 1.2.0).

BUG FIXES

    o Fix off-by-one error when processing 'S' in query_locs_to_ref_locs().


CHANGES IN VERSION 1.2.0
------------------------

NEW FEATURES

    o Add 'preprocess.reads' argument to "summarizeOverlaps" methods.

    o Add alphabetFrequencyFromBam().

SIGNIFICANT USER-LEVEL CHANGES

    o Export GappedReads() constructor.

    o coverage,Bamfile-method now returns empty RleList rather than NULL 

    o Add "mapCoords" and "pmapCoords" methods.

    o Defunct "map" and "pmap" methods (skip deprecation).

BUG FIXES

    o Bug fix in flipQuery().

    o Fix issue with "show" method for GAlignments and GAlignmentPairs objects
      when 'showHeadLines' global option is set to Inf.


CHANGES IN VERSION 1.0.0
------------------------

The first version of GenomicAlignments was included in Bioconductor 2.14. 
The package was created from existing code in IRanges, ShortRead, 
Rsamtools and GenomicRanges. 

NEW FEATURES

    o coverage,BamFile-method uses \code{yieldSize} to iterate through 
      large files

    o coverage,character-method calculates coverage from a BAM file

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