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Bioconductor Changlog.
Sat, 06 Sep 2008
Biostrings
Fixed a performance issue in "reverseComplement" methods for DNAStringSet/RNAStringSet/XStringViews that was introduced during the recent move of the "reverse" generic (+ some methods) to the IRanges package. Bumped version to 2.9.70
Biostrings
Fixed a performance issue in "reverseComplement" methods for DNAStringSet/RNAStringSet/XStringViews that was introduced during the recent move of the "reverse" generic (+ some methods) to the IRanges package. Bumped version to 2.9.70
added early version of "sort" method for XStringSet objects
Biostrings
Local low-level sorting C utilities are redundant with those defined in the IRanges package. Removed them and use those defined in IRanges instead. Bumped version to 2.9.69
Finished to remove the XStringList class and family (superseded by the XStringSet family).
Renamed replaceLetterAtLoc() -> replaceLetterAt() and renamed its 'loc' argument -> 'at'. Deprecated replaceLetterAtLoc(). Bumped version to 2.9.68
Added substr and substring methods for MaskedXString objects.
Biostrings
Minor code simplification change (added usage of replaceLetterAtLoc).
Biostrings
Allow users to specify integer, numeric, character, BString, and BStringSet objects as quality measures to the pairwiseAlignment function.
Biostrings
Added a check to ensure string qualities are of the same class during the alignment process.
Fixed issues in reverseComplement related to moving some reverse functionality to IRanges package.
Added new XStringQuality classes to make it easier to manage string quality information.
Biostrings
Added new XStringQuality classes to make it easier to manage string quality information.
Biostrings
Added a quality method for numeric error probabilities.
Biostrings
Updated the NEWS file to reflect recent changes.
Updated the coverage output for MIndex object to produce XInteger objects.
Modified coverage and slice to create XInteger and XIntegerViews respectively.
Moved function to IRanges package.
Biostrings
Moved XInteger and Views class definitions to IRanges and added XIntegerViews class.
Biostrings
Moved the reverse generic definition and the IRanges and MaskCollection methods to the IRanges package.
Added some alignment related classes to the export list.
Moved the coverage generic definition and the IRanges and MaskCollection methods to the IRanges package.
Biostrings
Minor doc change.
Biostrings
Small improvements to the "toComplex" method for DNAString objects. Got rid of almost all the [TODO] tags (only 3 left) in the documentation of the package and improved it quite a bit in many places.
Completed man page for XStringSet objects. Bumped version to 2.9.61
Completed man page for injectHardMask().
Added predefined RNA_GENETIC_CODE object and completed man pages for IUPAC_CODE_MAP and GENETIC_CODE.
Biostrings
Added predefined RNA_GENETIC_CODE object and completed man pages for IUPAC_CODE_MAP and GENETIC_CODE.
Modified example for matchPWM() so it works with new version of BSgenome.Dmelanogaster.UCSC.dm3 (starting with BioC 2.3, BSgenome data packages will contain masks that are active by default). Bumped version to 2.9.60
Biostrings
[merge -r 32724:32884 from the testing branch of Biostrings]
This merge includes:
o Addition of the 'dups0' slot to the ByPos_MIndex class: this allows a more
compact representation in memory of a ByPos_MIndex object that holds the
hits of a set of patterns that has a lot of duplicates. The benefit is
really noticeable when the patterns that are highly represented in the
original dictionary have a lot of hits which seems to be typically the
case when matching Solexa data against their reference genome. In this
case, using the new 'dups0' slot can make the ByPos_MIndex object about 3
times smaller.
o Take advantage of this new 'dups0' slot to improve the way duplicated
patterns are handle thru the "PDict -> matchPDict() -> MIndex" pipe. The
new strategy is to "remove them as early as possible and put them back as
late as possible". This leads to a gain in speed and also less memory is
needed to store the hits in the temporary buffer.
o Added a set of "coerce" methods for turning an arbitrary XStringSet object
into a BStringSet, DNAStringSet, RNAStringSet or AAStringSet instance (via
the as() function).
o Some internal rework of the BStringSet(), DNAStringSet(), RNAStringSet()
and AAStringSet() constructors (just cleaner code, no new feature).
o Added an "append" method for XStringSet objects. An important use case for
this is to put together a set of short reads and their reverse complements
in a single DNAStringSet object and then to turn this object into a single
PDict object (dual PDict object). Then this dual PDict object can be used
to walk each reference sequence only once (instead of twice) in order to
get the hits in both strands (+ and -).
o A couple of small corrections to the matchPDict() man pages.
Version bumped to 2.9.59
Added nucleotideSubstitutionMatrix function.
maskMotif(x, motif) now does not mask again what's already actively masked
Moved the MaskCollection class, its methods and the mask importation utilities (read.agpMask(), read.gapMask(), read.liftMask(), read.rmMask() and read.trfMask() functions) from this package to the IRanges package. Bumped version to 2.9.58
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
Biostrings
Moved the MaskCollection class, its methods and the mask importation utilities (read.agpMask(), read.gapMask(), read.liftMask(), read.rmMask() and read.trfMask() functions) from this package to the IRanges package. Bumped version to 2.9.58
Small cosmetic improvements at the C level. Started removing the XStringList class and family (superseded by the XStringSet family).
BiostringsCinterfaceDemo
Following the Biostrings/IRanges split, BiostringsCinterfaceDemo now needs to depend on and to import the new IRanges package.
[/BiostringsCinterfaceDemo] permanent link
Biostrings
[code cleaning] Use of macros in C code in charge of .Call entry points and C callable registration. This makes the code cleaner, shorter, and easier to read/maintain.
Removed Auto-Extending buffer local implementation. C code that deals with AE buffers is now calling the AE functions that are part of the IRanges C interface. Bumped version to 2.9.57
BiostringsCinterfaceDemo
Following the Biostrings/IRanges split, BiostringsCinterfaceDemo now needs to depend on and to import the new IRanges package.
[/BiostringsCinterfaceDemo] permanent link
Biostrings
Added "maskedwidth" and "maskedratio" methods for MaskedXString objects. Filled some gaps in man page for these objects.
Biostrings
Still need to export the "narrow", "reduce" and "gaps" methods (at least until the MaskCollection class + methods are moved to the IRanges package).
Changed pairwiseAlignment C code to reflect separation of IRanges from Biostrings.
Updated tests to reflect change in handling of aligning an empty string.
Use new_IRanges() from the IRanges C interface.
Moved the RoSeq stuff back from the IRanges package to this package (where it belongs).
Added checks for user interrupt to pairwise alignment code.
Fixed data type for pairwise alignment when one of the strings is empty.
Added const keywords in pairwiseAlignment C code to prevent inadvertent assignment.
Started to remove the IRanges stuff from the Biostrings package and to use the stuff that is defined in the new IRanges package instead. Version bumped to 2.9.55
Biostrings
Added some more parameter checks to stringDist and cleaned up its man page.
Updated STRING ALIGNMENT section of the NEWS file to reflect changes since last release.
Changed stringDist argument ignore.case to ignoreCase.
Added another set of examples to the stringDist man page.
Added a stringDist function to Biostrings.
Biostrings
Added a consmat method for AlignedXStringSet objects.
Biostrings
Added a consmat method for AlignedXStringSet objects.
Minor edit to consmat message.
Changed the show method of PairwiseAlignment and AlignedXStringSet classes to handle case when length(object) == 0.
Biostrings
Changed Frequency label to Probability in mismatchSummary function.
Fixed a bug in mismatchSummary when alignment is empty.
Fixed an argument check to pairwiseAlignment function.
Biostrings
Fixed xlab in exercise plot.
Removed usage (or reference) to pstricks tex style in BioC vignettes.
Change to show method for AlignedXStringSet objects.
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
Completed a "release candidate" for the alignments vignette.
Checked in some answers to the adapter example in the Alignments vignette.
Begun adding exercises to removing adapters from sequence reads section.
Minor text addition to Alignment vignette.
Added exercises for protein alignment in vignette.
Added exercises on edit distances to Alignment vignette.
Added another set of exercises to the Alignment vignette.
Changed some of the examples and added exercises to the Alignment vignette.
Removed unwanted names from the nchar method for PairwiseAlignmentSummary objects.
Added content to the Computation Profiling section of the Alignments vignette.
Biostrings
Added content to the Computation Profiling section of the Alignments vignette.
Added a bibliography to the Alignment vignette.
Added a Quality Assurance in Sequencing Experiments section to the Alignments vignette.
Biostrings
Added a Quality Assurance in Sequencing Experiments section to the Alignments vignette.
Added an errorSubstitutionMatrices function for instructional purposes.
Added a section illustrating the usage of BLOSUM and PAM matrices in pairwise sequence alignments.
Added a section on Removing Adapters from Sequence Reads to the alignment vignette.
Biostrings
Added a section on Removing Adapters from Sequence Reads to the alignment vignette.
Biostrings
Added more information of alignment functions and added a section on edit distances.
Changing the alphabet length for BString objects to 256 rather than the observed length in pairwiseAlignment.
1. Added a toString method for PairwiseAlignment objects.
2. Fixed a bug in mismatchTable & mismatchSummary to handle case when there are no mismatches.
3. Fixed a bug in pairwiseAlignment to handle case when there is only one character in a BString quality-based alignment.
Biostrings
Changed to descriptions of pairwise alignment in vignette.
Minor man page edit.
Biostrings
Added sample data sets to illustrate use of pairwiseAlignment on a small sample of short reads from a Solexa machine.
Switch memory allocation from R_alloc() to malloc()/free() in pairwiseAlignment to speed up calculations by avoiding swapping.
Fixed two bugs in mismatchSummary for QualityAlignedXStringSet objects:
1) Corrected integer overflow issue.
2) Corrected output when qualityType == "Solexa".
Optimized performance for pairwiseAlignment when scoreOnly = TRUE and gapOpening = 0.
Added more information to the vignette introduction.
Biostrings
latex tag change to get package to build.
Modifications to alignment documentation to begin discussion on new changes to code.
Biostrings
Further optimization of slice function.
Minor refactor to slice to make it more efficient.
Minor code fix to slice function.
Added a slice function for generating IRanges from coverage calculations.
Renamed whichRanges to whichAsRanges.
Added a whichRanges function that behaves like the which function, only it returns IRanges rather than integers.
[merge -r 32471:32660 from the testing branch of Biostrings] This merge from the testing branch introduces support of MTB_PDict objects (Multiple Trusted Band PDict objects) which can be used with matchPDict() for performing inexact matching with a small number of mismatching letters at any position in the individual patterns of the original dictionary. It also introduces the new "whichPDict" generic.
Biostrings
Fixed the weights argument in summary method for PairwiseAlignment arguments.
Fixed a bug in subsetting method for QualityAlignedXStringSet objects.
Expanded the range of qualityType for "Solexa" to [-5, 99].
Minor speed up enhancements to pairwiseAlignment function.
Minor speedup enhancements to alignment utility functions.
Biostrings
Added more information on qualityType to pairwiseAlignment man page.
Added the ability to handle Solexa quality scores in pairwise alignments.
Biostrings
Fixed a bug in mismatchSummary for AlignedXStringSet objects.
Moved calculation of nmatch for PairwiseAlignment objects down to C.
Modified coverage method for PairwiseAlignmentSummary to make it more efficient when start and end aren't supplied.