NEWS

---

GenomicAlignments 1.48.0

• No changes in this version.

GenomicAlignments 1.46.0

SIGNIFICANT USER-VISIBLE CHANGES

• The low-level CIGAR utilities and sequenceLayer() function are now in their own package, the cigarillo package, but with different names. Calling a low-level CIGAR utility function (or sequenceLayer()) defined in GenomicAlignments still works but issues a deprecation warning that indicates the name of the new function to use from cigarillo. For example: > cigarOpTable(c("18M4S", "8M2X5M2I10M")) M I D N S H P = X [1,] 1 0 0 0 1 0 0 0 0 [2,] 3 1 0 0 0 0 0 0 1 Warning message: In call_new_fun_in_cigarillo("cigarOpTable", "tabulate_cigar_ops", : cigarOpTable() is formally deprecated in GenomicAlignments >= 1.45.5 and replaced with the tabulate_cigar_ops() function from the new cigarillo package
• The package now depends on Seqinfo instead of GenomeInfoDb.

DEPRECATED AND DEFUNCT

• All the low-level CIGAR utilities and the sequenceLayer() function have moved to the new cigarillo package and are now deprecated in GenomicAlignments.

GenomicAlignments 1.44.0

• No changes in this version.

GenomicAlignments 1.42.0

• No changes in this version.

GenomicAlignments 1.40.0

NEW FEATURES

• Add 'seqinfo' argument to GAlignments() constructor function.

BUG FIXES

• mapToAlignments() S at start 0 coordinate fix. By Fedor Bezrukov. See https://github.com/Bioconductor/GenomicAlignments/pull/34
• Bugfix in isCompatibleWithSkippedExons() for single-end read alignments w/ more than 3 junctions. By Robert Castelo. See https://github.com/Bioconductor/GenomicAlignments/pull/32

GenomicAlignments 1.38.0

• No changes in this version.

GenomicAlignments 1.36.0

NEW FEATURES

• Add 'strandMode' argument to readGAlignmentsList() (contributed by Robert Castelo).

BUG FIXES

• Increase 'cigar_buf' size to reduce risk of buffer overflow in cigar-utils C code.

GenomicAlignments 1.34.0

BUG FIXES

• Fix buffer overflow in cigarNarrow()/cigarQNarrow() See commit 5d0a29b2795a95dfb006e8e54c7532b12bd5e79c.

GenomicAlignments 1.32.0

• No significant changes in this version.

GenomicAlignments 1.30.0

• No changes in this version.

GenomicAlignments 1.28.0

• No changes in this version.

GenomicAlignments 1.26.0

• No changes in this version.

GenomicAlignments 1.24.0

• No changes in this version.

GenomicAlignments 1.22.0

NEW FEATURES

• Add stackStringsFromGAlignments(). Analog to stackStringsFromBam() except that it stacks the read sequences stored in a GAlignments object instead of a BAM file.

BUG FIXES

• Fix summarizeJunctions() error when no junctions are found and 'genome' is specified.

GenomicAlignments 1.20.0

No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since

GenomicAlignments 1.18.0

GenomicAlignments 1.16.0

• Add coercion from list to GAlignmentsList.
• Improve performance of [[<- on GAlignmentsList objects. This is a 100x speedup or more on a big GAlignmentsList object.
• Remove spurious warning in summarizeOverlaps().

GenomicAlignments 1.14.0

SIGNIFICANT USER-VISIBLE CHANGES

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

• 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

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

GenomicAlignments 1.12.0

NEW FEATURES

• seqlevels() setter now supports "fine" and "tidy" pruning modes on GAlignmentsList objects (in addition to "coarse" mode, which is the default).
• Add "pcompare", "is.unsorted", "order", "sort", and "rank" methods for GAlignments objects.
• Add encodingHalves(), a low-level overlap encoding utility.

SIGNIFICANT USER-VISIBLE CHANGES

• Tweak behavior of isCompatibleWithSplicing() on paired-end encodings.
• 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.
• Speed up first() and last() on GAlignmentPairs object when the object has no names. Thanks to Pete Hickey for the suggestion.
• 2x to 3x speedup to "junctions" methods.

DEPRECATED AND DEFUNCT

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

BUG FIXES

• Make grglist() work on GAlignmentPairs object with strandMode set to 0. Thanks to Dario Strbenac for catching and reporting this.
• Fix bug affecting extractSteppedExonRanks() on certain paired-end encodings.
• Fix subsetting of OverlapEncodings objects and modernize their "show" method.

GenomicAlignments 1.10.0

NEW FEATURES

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

SIGNIFICANT USER-VISIBLE CHANGES

• The 'at' argument of pileLettersAt() is now expected to be a GPos object (GRanges still accepted).
• 50x speed-up of the granges() extractor for GAlignmentPairs object. The improvement is based on a suggestion by Arne Muller.

DEPRECATED AND DEFUNCT

• Remove left() and right() generics and methods (were defunct in BioC 3.3).
• Remove 'invert.strand' argument from "first" and "last" methods for GAlignmentPairs objects (was defunct in BioC 3.3).
• Remove strand() setter for GAlignmentPairs objects (was defunct in BioC 3.3).
• 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

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

GenomicAlignments 1.8.0

NEW FEATURES

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

SIGNIFICANT USER-VISIBLE CHANGES

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

DEPRECATED AND DEFUNCT

• After being deprecated in BioC 3.2, the left() and right() getters and strand() setter for GAlignmentPairs objects are now defunct.
• After being deprecated in BioC 3.2, the 'invert.strand' argument of the first() and last() getters for GAlignmentPairs objects are now defunct.
• After being deprecated in BioC 3.2, the 'order.as.in.query' argument of the "grglist" method for GAlignmentPairs objects is now defunct.
• 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.
• Remove the "mapCoords" and "pmapCoords" methods (were defunct in BioC 3.2).
• Remove the readGAlignment*FromBam() functions (were defunct in BioC 3.2).

BUG FIXES

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

GenomicAlignments 1.6.0

NEW FEATURES

• 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.
• The readGAlignment*() functions now allow repeated seqnames in the BAM header.
• Add "coverage" method for GAlignmentsList objects.
• The strand setter now works on a GAlignmentsList object in a restricted way (only strand(x) <- "+" or "-" or "*" is supported).

SIGNIFICANT USER-VISIBLE CHANGES

• summarizeOverlaps() now returns a RangedSummarizedExperiment object (defined in the new SummarizedExperiment package) instead of an "old" SummarizedExperiment object (defined in the GenomicRanges package).
• 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.
• Add 'real.strand' argument to first() and last() getters for GAlignmentPairs objects.

DEPRECATED AND DEFUNCT

• Deprecate left() and right() getters and strand() setter for GAlignmentPairs objects.
• Deprecate 'invert.strand' argument of first() and last() getters for GAlignmentPairs objects.
• Deprecate 'order.as.in.query' argument of "grglist" method for GAlignmentPairs objects.
• 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).
• After being deprecated in BioC 3.1, the "mapCoords" and "pmapCoords" methods are now defunct. mapToAlignments() should be used instead.
• 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

• 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.

GenomicAlignments 1.4.0

NEW FEATURES

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

SIGNIFICANT USER-VISIBLE CHANGES

• Add mapToAlignments(), pmapToAlignments(), mapFromAlignments(), and pmapFromAlignments() as replacements for the "mapCoords" and "pmapCoords" methods for GAlignments objects.
• Clarify use of 'fragments' in summarizeOverlaps() man page.
• Tweak "show" method for GAlignments objects to display a shorter version of long CIGARs.
• Add checks and more helpful error message for summarizeOverlaps() when "file does not exist"

DEPRECATED AND DEFUNCT

• Deprecated readGAlignment*FromBam() functions in favor of readGAlignments(), readGAlignmentPairs(), readGAlignmentsList() and readGappedReads().
• Deprecated "mapCoords" and "pmapCoords" methods.
• Removed Lngap(), Rngap(), introns(), and makeGAlignmentsListFromFeatureFragments() functions, and "ngap", "map", "pmap", and "splitAsListReturnedClass" methods (were defunct in GenomicAlignments 1.2.0).

BUG FIXES

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

GenomicAlignments 1.2.0

NEW FEATURES

• Add 'preprocess.reads' argument to "summarizeOverlaps" methods.
• Add alphabetFrequencyFromBam().

SIGNIFICANT USER-VISIBLE CHANGES

• Export GappedReads() constructor.
• coverage,Bamfile-method now returns empty RleList rather than NULL
• Add "mapCoords" and "pmapCoords" methods.
• Defunct "map" and "pmap" methods (skip deprecation).

BUG FIXES

• Bug fix in flipQuery().
• Fix issue with "show" method for GAlignments and GAlignmentPairs objects when 'showHeadLines' global option is set to Inf.

GenomicAlignments 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

• coverage,BamFile-method uses \code{yieldSize} to iterate through large files
• coverage,character-method calculates coverage from a BAM file