/usr/lib/R/site-library/GenomicAlignments/NEWS is in r-bioc-genomicalignments 1.6.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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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