Version: 1.48.0 Text: No changes in this version. Version: 1.46.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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 Version: 1.46.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The package now depends on Seqinfo instead of GenomeInfoDb. Version: 1.46.0 Category: DEPRECATED AND DEFUNCT Text: All the low-level CIGAR utilities and the sequenceLayer() function have moved to the new cigarillo package and are now deprecated in GenomicAlignments. Version: 1.44.0 Text: No changes in this version. Version: 1.42.0 Text: No changes in this version. Version: 1.40.0 Category: NEW FEATURES Text: Add 'seqinfo' argument to GAlignments() constructor function. Version: 1.40.0 Category: BUG FIXES Text: mapToAlignments() S at start 0 coordinate fix. By Fedor Bezrukov. See https://github.com/Bioconductor/GenomicAlignments/pull/34 Version: 1.40.0 Category: BUG FIXES Text: Bugfix in isCompatibleWithSkippedExons() for single-end read alignments w/ more than 3 junctions. By Robert Castelo. See https://github.com/Bioconductor/GenomicAlignments/pull/32 Version: 1.38.0 Text: No changes in this version. Version: 1.36.0 Category: NEW FEATURES Text: Add 'strandMode' argument to readGAlignmentsList() (contributed by Robert Castelo). Version: 1.36.0 Category: BUG FIXES Text: Increase 'cigar_buf' size to reduce risk of buffer overflow in cigar-utils C code. Version: 1.34.0 Category: BUG FIXES Text: Fix buffer overflow in cigarNarrow()/cigarQNarrow() See commit 5d0a29b2795a95dfb006e8e54c7532b12bd5e79c. Version: 1.32.0 Text: No significant changes in this version. Version: 1.30.0 Text: No changes in this version. Version: 1.28.0 Text: No changes in this version. Version: 1.26.0 Text: No changes in this version. Version: 1.24.0 Text: No changes in this version. Version: 1.22.0 Category: NEW FEATURES Text: Add stackStringsFromGAlignments(). Analog to stackStringsFromBam() except that it stacks the read sequences stored in a GAlignments object instead of a BAM file. Version: 1.22.0 Category: BUG FIXES Text: Fix summarizeJunctions() error when no junctions are found and 'genome' is specified. Version: 1.20.0 Category: No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since Text: Version: 1.18.0 Text: Version: 1.18.0 Category: No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since Text: Version: 1.16.0 Text: Version: 1.16.0 Category: NEW FEATURES Text: Add coercion from list to GAlignmentsList. Version: 1.16.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Improve performance of [[<- on GAlignmentsList objects. This is a 100x speedup or more on a big GAlignmentsList object. Version: 1.16.0 Category: BUG FIXES Text: Remove spurious warning in summarizeOverlaps(). Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: makeGAlignmentPairs() no more drops pairs with discordant seqnames. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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. Version: 1.14.0 Category: DEPRECATED AND DEFUNCT Text: 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). Version: 1.14.0 Category: BUG FIXES Text: Fix bug in pairing code of readGAlignmentPairs() when one mate in a pair is lost because of user-supplied filtering (e.g. mapqFilter=10). Version: 1.12.0 Category: NEW FEATURES Text: seqlevels() setter now supports "fine" and "tidy" pruning modes on GAlignmentsList objects (in addition to "coarse" mode, which is the default). Version: 1.12.0 Category: NEW FEATURES Text: Add "pcompare", "is.unsorted", "order", "sort", and "rank" methods for GAlignments objects. Version: 1.12.0 Category: NEW FEATURES Text: Add encodingHalves(), a low-level overlap encoding utility. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Tweak behavior of isCompatibleWithSplicing() on paired-end encodings. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Speed up first() and last() on GAlignmentPairs object when the object has no names. Thanks to Pete Hickey for the suggestion. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 2x to 3x speedup to "junctions" methods. Version: 1.12.0 Category: DEPRECATED AND DEFUNCT Text: Argument 'force' of seqinfo() and seqlevels() setters is deprecated in favor of new and more flexible 'pruning.mode' argument. Version: 1.12.0 Category: BUG FIXES Text: Make grglist() work on GAlignmentPairs object with strandMode set to 0. Thanks to Dario Strbenac for catching and reporting this. Version: 1.12.0 Category: BUG FIXES Text: Fix bug affecting extractSteppedExonRanks() on certain paired-end encodings. Version: 1.12.0 Category: BUG FIXES Text: Fix subsetting of OverlapEncodings objects and modernize their "show" method. Version: 1.10.0 Category: NEW FEATURES Text: 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. Version: 1.10.0 Category: NEW FEATURES Text: Add "invertStrand" method for GAlignmentPairs objects. Version: 1.10.0 Category: NEW FEATURES Text: Add 'use.names' argument to the "ranges", "granges", "grglist" and "rglist" methods for GAlignments and GAlignmentsList objects. Version: 1.10.0 Category: NEW FEATURES Text: Add 'use.names' argument to the "granges" and "grglist" methods for GAlignmentPairs objects. Version: 1.10.0 Category: NEW FEATURES Text: Add "ranges" method for GAlignmentPairs objects. Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The 'at' argument of pileLettersAt() is now expected to be a GPos object (GRanges still accepted). Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 50x speed-up of the granges() extractor for GAlignmentPairs object. The improvement is based on a suggestion by Arne Muller. Version: 1.10.0 Category: DEPRECATED AND DEFUNCT Text: Remove left() and right() generics and methods (were defunct in BioC 3.3). Version: 1.10.0 Category: DEPRECATED AND DEFUNCT Text: Remove 'invert.strand' argument from "first" and "last" methods for GAlignmentPairs objects (was defunct in BioC 3.3). Version: 1.10.0 Category: DEPRECATED AND DEFUNCT Text: Remove strand() setter for GAlignmentPairs objects (was defunct in BioC 3.3). Version: 1.10.0 Category: DEPRECATED AND DEFUNCT Text: 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). Version: 1.10.0 Category: BUG FIXES Text: Fix 'use.names=FALSE' in "grglist" and "rglist" methods for GAlignmentsList objects. Version: 1.8.0 Category: NEW FEATURES Text: Add coercion from GAlignments or GAlignmentPairs to DataFrame, and from GAlignmentsList to GAlignmentPairs. Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Use DESeq2 instead of DESeq in summarizeOverlaps examples (better late than never). Version: 1.8.0 Category: DEPRECATED AND DEFUNCT Text: After being deprecated in BioC 3.2, the left() and right() getters and strand() setter for GAlignmentPairs objects are now defunct. Version: 1.8.0 Category: DEPRECATED AND DEFUNCT Text: After being deprecated in BioC 3.2, the 'invert.strand' argument of the first() and last() getters for GAlignmentPairs objects are now defunct. Version: 1.8.0 Category: DEPRECATED AND DEFUNCT Text: After being deprecated in BioC 3.2, the 'order.as.in.query' argument of the "grglist" method for GAlignmentPairs objects is now defunct. Version: 1.8.0 Category: DEPRECATED AND DEFUNCT Text: 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. Version: 1.8.0 Category: DEPRECATED AND DEFUNCT Text: Remove the "mapCoords" and "pmapCoords" methods (were defunct in BioC 3.2). Version: 1.8.0 Category: DEPRECATED AND DEFUNCT Text: Remove the readGAlignment*FromBam() functions (were defunct in BioC 3.2). Version: 1.8.0 Category: BUG FIXES Text: seqnames() setter for GAlignments objects is now consistent with seqnames() setter for GRanges objects. Version: 1.6.0 Category: NEW FEATURES Text: 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. Version: 1.6.0 Category: NEW FEATURES Text: The readGAlignment*() functions now allow repeated seqnames in the BAM header. Version: 1.6.0 Category: NEW FEATURES Text: Add "coverage" method for GAlignmentsList objects. Version: 1.6.0 Category: NEW FEATURES Text: The strand setter now works on a GAlignmentsList object in a restricted way (only strand(x) <- "+" or "-" or "*" is supported). Version: 1.6.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: summarizeOverlaps() now returns a RangedSummarizedExperiment object (defined in the new SummarizedExperiment package) instead of an "old" SummarizedExperiment object (defined in the GenomicRanges package). Version: 1.6.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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. Version: 1.6.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Add 'real.strand' argument to first() and last() getters for GAlignmentPairs objects. Version: 1.6.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate left() and right() getters and strand() setter for GAlignmentPairs objects. Version: 1.6.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate 'invert.strand' argument of first() and last() getters for GAlignmentPairs objects. Version: 1.6.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate 'order.as.in.query' argument of "grglist" method for GAlignmentPairs objects. Version: 1.6.0 Category: DEPRECATED AND DEFUNCT Text: 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). Version: 1.6.0 Category: DEPRECATED AND DEFUNCT Text: After being deprecated in BioC 3.1, the "mapCoords" and "pmapCoords" methods are now defunct. mapToAlignments() should be used instead. Version: 1.6.0 Category: DEPRECATED AND DEFUNCT Text: 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!" Version: 1.6.0 Category: BUG FIXES Text: 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. Version: 1.4.0 Category: NEW FEATURES Text: All "findOverlaps" methods now support 'select' equal "last" or "arbitrary" (in addition to "all" and "first"). Version: 1.4.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Add mapToAlignments(), pmapToAlignments(), mapFromAlignments(), and pmapFromAlignments() as replacements for the "mapCoords" and "pmapCoords" methods for GAlignments objects. Version: 1.4.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Clarify use of 'fragments' in summarizeOverlaps() man page. Version: 1.4.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Tweak "show" method for GAlignments objects to display a shorter version of long CIGARs. Version: 1.4.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Add checks and more helpful error message for summarizeOverlaps() when "file does not exist" Version: 1.4.0 Category: DEPRECATED AND DEFUNCT Text: Deprecated readGAlignment*FromBam() functions in favor of readGAlignments(), readGAlignmentPairs(), readGAlignmentsList() and readGappedReads(). Version: 1.4.0 Category: DEPRECATED AND DEFUNCT Text: Deprecated "mapCoords" and "pmapCoords" methods. Version: 1.4.0 Category: DEPRECATED AND DEFUNCT Text: Removed Lngap(), Rngap(), introns(), and makeGAlignmentsListFromFeatureFragments() functions, and "ngap", "map", "pmap", and "splitAsListReturnedClass" methods (were defunct in GenomicAlignments 1.2.0). Version: 1.4.0 Category: BUG FIXES Text: Fix off-by-one error when processing 'S' in query_locs_to_ref_locs(). Version: 1.2.0 Category: NEW FEATURES Text: Add 'preprocess.reads' argument to "summarizeOverlaps" methods. Version: 1.2.0 Category: NEW FEATURES Text: Add alphabetFrequencyFromBam(). Version: 1.2.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Export GappedReads() constructor. Version: 1.2.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: coverage,Bamfile-method now returns empty RleList rather than NULL Version: 1.2.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Add "mapCoords" and "pmapCoords" methods. Version: 1.2.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Defunct "map" and "pmap" methods (skip deprecation). Version: 1.2.0 Category: BUG FIXES Text: Bug fix in flipQuery(). Version: 1.2.0 Category: BUG FIXES Text: Fix issue with "show" method for GAlignments and GAlignmentPairs objects when 'showHeadLines' global option is set to Inf. Version: 1.0.0 Category: The first version of GenomicAlignments was included in Bioconductor 2.14 Text: Version: 1.0.0 Category: The package was created from existing code in IRanges, ShortRead Text: Version: 1.0.0 Category: Rsamtools and GenomicRanges Text: Version: 1.0.0 Category: NEW FEATURES Text: coverage,BamFile-method uses \code{yieldSize} to iterate through large files Version: 1.0.0 Category: NEW FEATURES Text: coverage,character-method calculates coverage from a BAM file