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Bioconductor Changlog.
Tue, 13 Oct 2009
BiostringsCinterfaceDemo
Additional examples and code clean-up
- read_solexa_fasta for reading two-line fasta files
- alphabet_by_cycle for tallying nucleotide counts by solexa cycle
- reorganize interface and documentation
[/BiostringsCinterfaceDemo] permanent link
BiostringsCinterfaceDemo
aligned with latest changes to the Biostrings C interface
[/BiostringsCinterfaceDemo] permanent link
BiostringsCinterfaceDemo
Made changes required because of recent move of the Auto-Extending buffers (C level facilities) from the Biostrings to the IRanges package. Bumped version to 0.1.5
[/BiostringsCinterfaceDemo] permanent link
BiostringsCinterfaceDemo
trying to please 'R CMD check'
[/BiostringsCinterfaceDemo] permanent link
BiostringsCinterfaceDemo
added the BiostringsCinterfaceDemo package
[/BiostringsCinterfaceDemo] permanent link
BiostringsCinterfaceDemo
Following the Biostrings/IRanges split, BiostringsCinterfaceDemo now needs to depend on and to import the new IRanges package.
[/BiostringsCinterfaceDemo] permanent link
BiostringsCinterfaceDemo
Following the Biostrings/IRanges split, BiostringsCinterfaceDemo now needs to depend on and to import the new IRanges package.
[/BiostringsCinterfaceDemo] permanent link
Biostrings
Reworked the core constructors BString(), BStringList() and families: better semantic (via the new start and nchar args), better speed (on character input for now, other type of input will follow) and better internal code. Time to bump.
Biostrings
Added more genomes to phage data set and composed examples using them.
Biostrings
Add more information to PairwiseAlignmentSummary show output.
Minor change to mismatchSummary function.
Created a PairwiseAlignmentSummary class to make it easier for users to get summaries of fitted pairwise alignments.
Added nmatch and nindel functions.
Added a weight argument to mismatchSummary function.
Minor change to man page.
Minor speedup to mismatchSummary method for PairwiseAlignment objects.
Biostrings
Small improvements to XStringSet basic capabilities:
- added "width" and "narrow" methods for character vectors;
- added "threebands" method for character and XStringSet objects;
- improved XStringSet-class.Rd man page;
- modified PDict() constructor to use "threebands" (for XStringSet)
internally for splitting the input dict into head+tb+tail parts.
Bumped version to 2.11.28
Biostrings
Minor code change to use accessor function in internal code.
Biostrings
Bumped version to 2.13.22 in order to release the new code for fast matching of the head/tail of a PDict object. In some situations where the head/tail is very narrow (<= 8b in total), the overall speed up for matchPDict() can be 10x or more.
Biostrings
added some references to the man pages for PDict/matchPDict
Biostrings
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Added "width" method for MIndex objects.
Renamed ByName_MIndex class -> SparseMIndex and completely turned off
any code related to this class (the SparseMIndex class is not used
anymore, but might be needed again in the future). As a side effect,
'R CMD check' is now totally happy.
Fixed bug in consensusMatrix() when some of the values passed thru the 'shift' arg were <= - 'width'.
small improvement to man/nucleotideFrequency.Rd
Biostrings
Added another condition for a valid alignment.
Biostrings
fixed a typo
added transcribe and cDNA as functions
that were missing
Biostrings
Speed up "countIndex" method for MIndex objects (by using new
"elementLengths" method for list objects).
Bumped version to 2.13.14
Biostrings
Renamed consmat consensusMatrix and deprecated consmat.
Added a baseOnly argument to the consmat method for PairwiseAlignment objects.
Removing the consmat method for AlignedXStringSet objects since it makes little sense.
Optimized performace of consmat function.
Biostrings
Replaced notion of inserts with indels in pairwiseAlignments since this information represents either insertions or deletions.
Biostrings
First pass as reworking the pairwiseAlignment infrastructure to use less memory. It is also marginally faster as well.
Biostrings
Minor changes to function descriptions.
Add creation of PairwiseAlignment from strings to the examples section.
Biostrings
Sped up computation in pairwise alignment by better approach to allocate memory.
Revered back to using R_alloc in pairwise alignment functionality.
I removed the now irrelevant old email: "WolfgangUseCase.txt".
I removed the capricious use "pstricks.sty" in the vignette.
Minor edits to Alignment vignette to get it into "release" quality.
Biostrings
Fixed serious bug in vcountPDict(): except for the 1st column of the returned matrix (where all match counts seem to have been correctly reported), in all other columns the match count for any duplicated pattern was always reported to be 0. Bumped version to 2.11.29
Biostrings
Changing pairwiseAlignment's gapExtension default value to -2.
Modified calculation of profile to mean start of alignment rather than first substitution.
Biostrings
Fixed the traceback when insertions are immediately followed by a deletion and vice versa in pairwiseAlignment.
Biostrings
Reduced size of data used with vcountPDict() in matchprobes.Rnw vignette so it has a chance to work on Windows too. In the same vignette, use CL2001032020AA.cel now in affydata (added in >= 1.11.4) instead of the one found in (deprecated) matchprobes package. Fixed typo in matchPWM.Rd. Bumped version to 2.11.32
Biostrings
matchPWM(): When passed a Position Weight Matrix of doubles, matchPWM()
doesn't coerce it to an integer matrix anymore. The same apply to its
'min.score' argument. PWMscoreStartingAt() now always returns a vector
of doubles, whatever the storage mode of the PWM was (this could be
Bumped version to 2.13.1
Biostrings
Added safe (and user-friendly) "IRanges" and "Mask" constructors. Reworked the examples in MaskedXString-class.Rd. Some other samll fixes and improvements.
Deprecated the needwunsQS function and added more information in the Alignments.Rnw vignette on optimal pairwise alignments.
Fixed some problems with the "names<-" method for IRanges object. Added "names<-" method for MaskCollection objects. Bumped version to 2.7.54
Fixed latex issue.
Clarified what quality1 and quality2 arguments represent.
Biostrings
put back fastaEx from Biostrings1
Renamed Exfiles/ folder as extdata/. No version bump.
Biostrings
sync up with the RELEASE_2_3 branch
Biostrings
Modified replaceLetterAt() example.
Some improvements to replaceLetterAt():
- added support for logical or Rle 'at' argument in "replaceLetterAt"
method for DNAString objects;
- added a "replaceLetterAt" method for DNAStringSet objects (with the
current restrictions that 'x' and 'at' must be rectangular i.e. 'x'
must have a constant width and 'at' must be a logical matrix with
the same dimensions as 'x').
Bumped version to 2.13.8
Fixed coverage method for PairwiseAlignedFixedSubjectSummary objects.
Biostrings
Fixed bug causing XStringViews_match_TBdna() to report wrong match ending positions for duplicated patterns. Bumped version to 2.9.16
Biostrings
Finished adding code to support the endGap argument to pairwiseAlignment.
Biostrings
Minor typo fixes.
finished to resync code with new XInteger class definition
bumped version to 2.9.72
Biostrings
Added codes, codec, enc_lkup, and dec_lkup methods for XStringSet classes.
Minor change in terminology from match to align in code.
Added "matchPDict" methods for XStringViews and MaskedXString objects (only for a DNA input sequence). Version bumped to 2.9.10
Biostrings
Added the countPDict() function: faster than matchPDict() if getting the
number of matches is what matters only (without regarding their positions),
especially when there is a high number of matches.
Version bump.
Biostrings
updating the consmat manual page
adding the FASTA files for two yeast genes
Added "as.character" and "consmat" methods for "BStringAlign" objects. No version bump.
Version finally bumped after a series of changes:
o matchPattern.Rnw vignette replaced by much improved GenomeSearching.Rnw
vignette (still a work-in-progress).
o reverse(), complement() and reverseComplement() now preserve desc(x) when
applied to BStringViews object x.
o matchPDict() now returns a PDictMatches object (new class) instead of a list
of integer vectors. The user can then subset this PDictMatches object with [[,
convert it into a list of integer vectors with as.list, or convert it into a
set of views on the original subject with extractMatches(). Other functions
can (and will) be added later in order to provide a wider choice of
efficient conversion/extraction tools.
WARNING: This is still a work-in-progress. Function names and semantics are
not yet stabilized!
Biostrings
More work on the PDict() constructor (changed its signature, the length of the Trusted Dictionary must now be specified via the 'tb.width' arg instead of the 'tb.end' arg). Version bumped to 2.7.23.
Biostrings
Don't use the ByName_MIndex class anymore (will be removed soon). MIndex objects returned by matchPDict() (and family) are now always of subtype ByPos_MIndex (used to be ByName_MIndex if the 'pdict' arg had names).