NEWS
girafe 1.21.1
- replaced seq_name method by seqnames
(due to deprecation of seq_name generic)
girafe 1.3.11
- When reducing overlapping reads, the read counts are now directly
taken into account as weights for deriving the consensus sequence.
To that aim, a custom function "weightedConsensusMatrix" is now
used in place of "consensusMatrix" from Biostrings
girafe 1.3.8
- Several minor changes including corrections to the documentation.
For plotting the aligned reads, the user can now specify custom
colours for certain types of annotated feature. See
?plotAligned
for an example and details.
girafe 1.3.6
- New function "countReadsAnnotated" to sum up aligned reads per
category of genome feature (i.e. gene, ncRNA, etc.).
- New function "medianByPosition" that allows for a
memory-efficient computation of the median base quality
at each nucleotide position in the reads
girafe 1.3.5
- Changed implementation of 'sample' method. The 'Rle' objects
used before were not suitable for large AlignedGenomeIntervals
objects. 'sample' now uses the base::sample.int function. As
a consequence only sampling with replacement is possible for
the moment.
- Added a logical argument 'both' to the 'fracOverlap' function.
IF TRUE (default), both overlapping partners must be involved
to at least a proportion of 'min.frac' in order to report the
overlap; if FALSE, it suffices that one of the partners meets
the 'min.frac' requirement.
girafe 1.3.4
- Added an argument 'method' for the 'reduce' function. This
argument supersedes the boolean argument 'exact', use
'method="exact"' in place of 'exact=TRUE'. Additional options
are 'method="same5"' and 'method="same3"' to combine intervals
that have the same 5' or 3'end, respectively.
- Added a "fasta" format option to the export method for
AlignedGenomeIntervals objects.
girafe 1.3.2
- Added slot 'chrlengths' to S4 class 'AlignedGenomeIntervals'
This optional slot stores a named integer vector of
chromosome lengths. If present, it is used by 'coverage' and
other methods, instead of obtaining those chromosome lengths
from the annotation package indicated by the 'organism' slot.
- Added an "export" method for objects of classes
"Genome_intervals" and "Genome_intervals_stranded"
girafe 1.1.15
- Certain functions (reduce, interval_overlap, fracOverlap)
got an extra argument 'mem.friendly' that if set to TRUE
(default: FALSE) leads to the data broken down into
chromosome-wise batches for the computations, and thus
for a "memory-friendlier", but slower, version of these
computations.
girafe 1.1.12
- Added a new function 'agiFromBam' which uses Rsamtools
for creating AlignedGenomeIntervals objects directly
from BAM files
girafe 1.1.6
- Added an 'id' slot to AlignedGenomeIntervals objects, which
allows users to assign a custom identifier to each interval
girafe 1.1.5
- Added a 'sample' method for AlignedGenomeIntervals objects
Consists of drawing a random sample of n of the aligned reads
and returning the AlignedGenomeIntervals object defined by
these aligned reads
girafe 1.1.3
- Added a NEWS file
- added a 'sort' method for AlignedGenomeIntervals to sort them
by chromosome number > start position > end position
- added a 'hist' method for AlignedGenomeIntervals which creates
a histogram of the lengths of the reads aligned to the intervals
Like the 'hist' function from package graphics, it returns an
object of class 'histogram' and accepts the argument 'plot=FALSE'
girafe 1.1.2
- in function 'fracoverlap', the argument 'min.frac' now applies
to both intervals and specifies the minimum required fraction of
each of the two interval widths by which two intervals should
overlap in order to be marked as truly overlapping (before: only
applied to the shorter of the two intervals)