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Bioconductor Changlog.
Wed, 23 Jul 2008
ShortRead
srdistance now returns distances, i.e., >= 0
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.
GenomeGraphs
Added Rd files for makeTranscript, makeGene and makeGeneRegion
[/GenomeGraphs] permanent link
xcms
fixed some documentation prolems