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Bioconductor Changlog.
Fri, 09 May 2008
Biostrings
Added the read.liftMask() function for reading a mask of "inter-contig gaps" from an UCSC "lift" file. No version bump.
Fixed the profile calculation method in pairwiseAlignment.
Biostrings
Added the read.rmMask() and read.trfMask() functions for reading a mask from a RepeatMasker .out file or from a Tandem Repeats Finder .bed file. No version bump yet.
Added score profiles to pairwiseAligment results to allow users to see how well strings align at different points.
Biostrings
Added the maskMotif() generic function for masking a sequence by content.
As a consequence, previous 'masks(x) <- "motif"' syntax must be replaced by
new 'x <- maskMotif(x, "motif")' syntax.
Bumped version to 2.9.3
Biostrings
Added the coverage() generic function with methods for IRanges, MaskCollection, XStringViews, MaskedXString and MIndex objects. Version bumped to 2.9.2
Changed the algorithm in pairwiseAlignment to start at the end of the strings rather than the beginning to make it easier to get the scores based on alignment starts.
First pass as reworking the pairwiseAlignment infrastructure to use less memory. It is also marginally faster as well.
Biostrings
First pass as reworking the pairwiseAlignment infrastructure to use less memory. It is also marginally faster as well.
Biostrings
Better fix for adjacentViews.
Fixed a bug in adjacentViews to allow the handling of character vectors.
Biostrings
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Fixed a typo in man file.
Fixed the definition of XStringAlign class.
Set default for readFASTA() 'strip.desc' arg to TRUE (with a warning if the arg is missing).
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
Added the "alphabetFrequency" and "oligonucleotideFrequency" methods for MaskedXString objects. Started completing the man page for MaskCollection.
Biostrings
Finished adding code to support the endGap argument to pairwiseAlignment.
Biostrings
Finished adding code to support the endGap argument to pairwiseAlignment.
Added an endGap argument to pairwiseAlignment to allow users to ignore end gaps when performing pairwise alignments.
Biostrings
Renamed the BStringViews class -> XStringViews (long due change!). Bumped version to 2.7.52.
Implemented the quality-based substitution matrix method of Ketil Malde.
Biostrings
Implemented the quality-based substitution matrix method of Ketil Malde.
Biostrings
Removing integer specification from substitution matrix.
Allow users to specify XString objects for the string quality scores in pairwiseAlignment.
Modified how character based quality scores are converting into [0, 1] metrics during pairwiseAlignment.
Added the ability to use characters for the quality measures of the strings in pairwiseAlignment.
To the pairwiseAlignment function:
1) Added a scoreOnly parameter for returning just the score (and not that alignment).
2) Renamed matchScoring parameter to substitutionMatrix.
Biostrings
To the pairwiseAlignment function:
1) Added a scoreOnly parameter for returning just the score (and not that alignment).
2) Renamed matchScoring parameter to substitutionMatrix.
Biostrings
Minor man file edit.
Added the ability to specify quality measures for the strings when performing pairwise alignments.
Biostrings
Added basic support for Position Weight Matrix matching thru the new matchPWM() and countPWM() functions. Also added related utility functions maxWeights(), maxScore() and PWMscore(). See ?matchPWM for the details. Bumped version to 2.7.47.
Minor edits to the description and details section of the man file.
Disabled update() of NormalIRanges objects and fixed a small problem with the "update" method for IRanges objects.
Added "isEmpty", "max" and "min" methods for IRanges/NormalIRanges objects. Disabled subsetting and narrowing of NormalIRanges objects (these operations do NOT preserve normality in general). Small improvement to the "gaps" semantic and implementation.
Biostrings
Added "isEmpty", "max" and "min" methods for IRanges/NormalIRanges objects. Disabled subsetting and narrowing of NormalIRanges objects (these operations do NOT preserve normality in general). Small improvement to the "gaps" semantic and implementation.
Performance optimization of the pairwiseAlignment function.
Added more information into the XStringAlign class to provide users with better information on the alignment.
Renamed the C file containing pairwise alignment code to get it to conform to package conventions and minor cleanup edits.
Added the ability to handle affine gaps in pairwiseAlignment.
Biostrings
A first pass at a function for generating global, local, and overlap pairwise alignments. This new pairwiseAlignment function expands on the needwunsQS function.
Replaced previous MaskedXString draft by a better design for the MaskedXString
family of containers. This is a deep change in how masking sequences is handled.
Needed to make lots of internal changes and additions in order to support this
new masking mechanism. Version bumped to 2.7.45
Biostrings
matchPDict() now supports IUPAC ambiguities in the subject i.e. it will
treat them as wildcards when called with 'fixed=FALSE' on a Trusted Band
dict or with 'fixed=c(pattern=TRUE, subject=FALSE)' on any dict.
The implementation of this new feature uses a "split and merge pointers"
technique while walking the Aho-Corasick tree. Some testing, benchmarks,
code optimization and cleaning are still required. In particular it
needs to be tested on a genome with injected SNPs.
Version bump -> 2.7.44
BiostringsCinterfaceDemo
trying to please 'R CMD check'
[/BiostringsCinterfaceDemo] permanent link
Biostrings
Renamed 'data' slot (XString class) -> 'xdata'. Version bumped to 2.7.43
Biostrings
Added the "alphabet" method for "XStringSet" objects + a few additions to the TODO file. Version bumped to 2.7.42.
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
Thu, 27 Mar 2008
Biostrings
added the lettersToAmbiguity() utility function
Fixed "reduce" method for .IRanges objects and "mask" method for IRanges objects (both were broken on .IRanges/IRanges objects with names). Version bump.
BiostringsCinterfaceDemo
added the BiostringsCinterfaceDemo package
[/BiostringsCinterfaceDemo] permanent link
Biostrings
Added "chartr" method for XStringSet and BStringViews objects. Some small changes and additions to the C interface. Bumped version to 2.7.39.
Biostrings
Added next_XStringSet_elt_asRoSeq() to the C interface and use it in C function XStringSet_char_frequency() to speedup "alphabetFrequency" methods for XStringSet objects (4x speedup). Bumped version to 2.7.38.
more small improvements to alphabetFrequency() based on Martin's feedback
small improvements to alphabetFrequency() based on Martin's feedback
[again] The additional 15x speedup for alphabetFrequency() on XStringSet objects when 'collapse' is TRUE turned out to be broken. Removed it.
No, the additional 15x speedup for alphabetFrequency() on XStringSet objects when collap
Fixed small problem in alphabetFrequency() when 'freq' is TRUE.
Polishing alphabetFrequency() for an additional speedup of 15x on XStringSet objects when 'collapse' is TRUE.
Reworked alphabetFrequency() (most of it is now done in C). The new implementation is > 250x faster on XStringSet objects.
Biostrings
Added utility functions alloc_XStringSet() and write_RoSeq_to_XStringSet_elt() (part of the C interface) for creating an XStringSet instance in 2 steps: first create the skeleton (with junk data in it), then fill it with some input character data (typically read from a file). Version bumped to 2.7.36
Biostrings
Fixed serious memory corruption bug in the C code in charge of low-level manipulation of the extendable buffers (thanks Martin for finding this one). Bumped version to 2.7.35.
Biostrings
version bumped to 2.7.34
Biostrings
bumped version to 2.7.32
Biostrings
Reworked the class hierarchy:
- Added the .IRanges class (not exported): now the IRanges class is just
the exported version of the .IRanges class (it derives directly from
it without any additional slot). Replacement methods "start<-",
"end<-" and "width<-" are only defined for IRanges objects so the user
cannot use them to modify a .IRanges object. Therefore the "safe" .IRanges
class can be used to make the BStringSet class (and family) "safe" too by
deriving it from .IRanges and not IRanges (see below).
- Reorganized the hierarchy of the BString class and subclasses by adding
the XString virtual class: now the BString, DNAString, RNAString and
AAString classes are all direct XString subtypes with no additional slots.
Most importantly, they are all at the same level in the new hierarchy
i.e. DNAString, RNAString and AAString objects are NOT BString objects
anymore.
- Reorganized the BStringSet and BStringList families of classes in a
similar way by adding the XStringSet and XStringList virtual classes.
Also now the XStringSet class derives from the .IRanges class instead of
the IRanges class so it is "safe".
- Added the XString() and XStringSet() versatile constructors. The BString()
and BStringSet() constructors and families are now based on them.
- Renamed subBString() -> subXString() and deprecated subBString().
No version bump yet.
Biostrings
Updated the Depends and Suggests fields and changed the license from LGPL to Artistic-2.0.
Renamed IntIntervals class -> IRanges. Version bumped to 2.7.31
Biostrings
cosmetic
- Added the intToIntervals(), intToAdjacentIntervals() and narrow() functions for
creating or modifying IntIntervals objects. Those functions together with the
restrict() function added previously are used by the BStringList() and BStringSet()
constructors and family.
- Fixed a nasty bug in the narrow_BStringList() C function.
- Some additions and improvements at the C level.
- No version bump yet.
Biostrings
[comments for previous commit + this commit]
- Added the trim() function for trimming the "out of limits" views of a
BStringViews object.
- Now the BStringSet() constructor (and family):
(1) fully supports BStringViews input,
(2) has a 'use.names' argument.
- Support the 'use.names' argument in the "unlist" method for ViewsIndex
objects.
Biostrings
Added the chartr() generic function with a method for BString objects.
Methods for other types of objects (in particular for BStringViews and
BStringSet objects) will come later.
Version bump.
Versatile constructor RNAString() (resp. DNAString()) now converts from DNA
to RNA (resp. RNA to DNA) by replacing T by U (resp. U by T) instead of
trying to mimic transciption. This conversion is still performed without
copying the sequence data and thus remains very fast.
Also the semantic of comparing RNA with DNA has been changed to remain
consistent with the new semantic of RNAString() and DNAString() e.g.
RNAString("UUGAAAA-CUC-N") is considered equal to DNAString("TTGAAAA-CTC-N").
Version bumped to 2.7.26
Biostrings
Added the 'collpase' arg to alphabetFrequency() and family. Version bump.
Biostrings
More work on the PDict() constructor (now supports almost all kind of Trusted Band dictionaries, not only Trusted Prefix dictionaries, cropping the input sequences via the tb.start/tb.end/tb.width args is almost fully implemented). matchPDict() not yet ready to accept PDict objects with a head. Renamed the ULdna_PDict class -> CWdna_PDict. Version bumped to 2.7.24.
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
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.