CHANGES IN VERSION 1.12.3 ------------------------- BUG FIXES o FastqSampler obeys R's random number seed CHANGES IN VERSION 1.12.1 ------------------------- BUG FIXES o qa report scales adapterContamination correctly o FastqSampler would rarely sample fewer than requested reads o FastqSampler supports outputs of >2^31 - 1 total nucleotides CHANGES IN VERSION 1.11 ----------------------- NEW FEATURES o trimTails to trim low quality trailing nucleotides o trimEnds to remove arbitrary (vectors of) letters from reads or qualities o FastqStreamer to iterate over a fastq file o FastqFile, FastqFileList to represent fastq files SIGNIFICANT USER-VISIBLE CHANGES o writeFastq has argument full, default value FALSE, disabling printing of identifier a second time in '+' line o srapply requires that options(srapply_fapply="parallel") or options(srapply_fapply="Rmpi") to enable parallel processing via fapply BUG FIXES o SolexaRealign, SolexaAlign, and SolexaResult transposed strand inforamtion o FastqSampler segfaulted on some files o writeFasta had a semi-documented argument mode; it is now documented and as a consequence dis-allows argument 'append' that would previously have been passed to underlying methods. CHANGES IN VERSION 1.9 ---------------------- NEW FEATURES o Support for HiSeq tile layout o Track reads passing filters, including across logical filter operations CHANGES IN VERSION 1.7 ---------------------- BUG FIXES o qa() represented the per-cycle quality scores incorrectly; this influenced qa[["perCycle"]][["quality"]][["Score"]], but not the qa report. o qa() for type="SolexaExport" transposed the 'aligned' and 'filtered' labels on all elements of SolexaExportQA. Thanks Nicolas Delhomme for the report. o report() failed when each read was unique. Thanks Peng Yu for the report. SIGNIFICANT USER-VISIBLE CHANGES o The perCycleQuality graph in the qa report now includes boxplots for all cycles instead of just the median value. o A depthOfCoverage graph has been added to the qa report for BAM, Bowtie, SolexaExport and SolexaRealign file types. o An adapterContamination measure has been added to the qa report for BAM, Bowtie, SolexaExport, SolexaRealign and Fastq file types. o srorder is now stable (the original order of identical is preservered). NEW FEATURES o Add class BAMQA. qa() can now be called on BAM files. o The param argument in readAligned() and qa() for type="BAM" can now be a single ScanBamParam object or a list of them. o FastqSampler can be used to draw samples from a fastq file. CHANGES IN VERSION 1.5 ---------------------- SIGNIFICANT USER-VISIBLE CHANGES o levels(strand(aln)) is c("+", "-", "*") (was c("-", "+", "*")) o Add USE.NAMES argument to srapply, minimum length to (internal) function ..reduce. NEW FEATURES o Optionally retrieve multiplex bar code, paired read number, and id from SolexaExport (contribution from Nicolas Delhomme) o renew() and renewable() provide an interface to updating ShortRead instances o srapply checks for and uses multicore o readIntensities supports Illumina RTA '.cif' / '.cnf' files o readAligned type="BAM" parses BAM files, extracting simple (no indel) cigars BUG FIXES o readIntensities type="IparIntensity" correctly handles multiple tiles CHANGES IN VERSION 1.3 ---------------------- SIGNIFICANT USER-VISIBLE CHANGES o coverage,AlignedRead-method has a changed interface (shift/width rather than start/end) and default behavior (return value in genome coordinates, rather than minimal covered region). o readAligned,character-method, type="Bowtie" and readFastq return FastqQuality by default. o coverage,AlignedRead-method now returns an RleList NEW FEATURES o qa reports from _realign.txt, MAQMap files o QualityScoreDNAStringSet coercion methods o qa type="character" now accepts a filter argument with value srFilter() o alphabetByCycle supports variable-width XStringSets o qa,ShortReadQ and qa,list methods for qa on existing objects BUG FIXES o Parse .gz realign files o alphabetScore,FastqQuality-method shifted quality by +1 CHANGES IN VERSION 1.1 ---------------------- SIGNIFICANT USER-VISIBLE CHANGES o 454 quality scores are returned as FastqQuality-encoded o For functions accepting dirPath, pattern to name files, allow dirPath to be a vector of file names when pattern is character(). o width() on ShortRead and derived classes (including AlignedRead now returns a vector of widths, of length equal to the length of the object. NEW FEATURES o Add Bowtie as a 'type' value for qa and report o Add dustyScore() and dustyFilter() to identify low-complexity regions o Parse _qseq files (to ShortReadQ or XDataFrame) o Parse IPAR image intensity files _int.txt.p, _nse.txt.p, _pos.txt o Create HTML-based quality assessment reports o Add trimLRPatterns() for ShortRead and derived classes (ShortReadQ, AlignedRead). o Add narrow() for ShortRead, QualityScore, and derived classes. o Use append() to append two objects of the same ShortReadQ or QualityScore and derived classes together o writeFastq for classes derived from ShortReadQ o Input functions support .gz or text files. o readIntensity reads Solexa image intensity files into R, including information about lane, tile, x, and y coordinates of each read. o readPrb returns different types of objects, depending on the 'as' argument of the readPrb,character-method. o readXStringSet gets arguments skip, nrows; argument order changed slightly o New built-in SRFilters positionFilter, uniqueFilter to select reads aligning to particular positions, or to select only unique instances of reads aligning to each position. o readAligned gains a Solexa _results parser (_results files are listed as 'intermediate' in the Solexa manual, and not a good end-point for analysis) o readAligned gains a Bowtie output parser o readAligned gains ability to parse MAQ 0.7 version binary files BUG FIXES o readQual would fail to read 454 quality scores correctly when these spanned more than one line of input per read o coverage treated reads as 1 base longer than they were o FastqQuality got the quality encoding off by one in as(x, "matrix") o qa_solexa.Rnw incorrectly displayed read occurences when lanes were presented out-of-order (an unusual occurence) o readAligned SolexaAlign, etc., updated to parse 'chromsome' and 'position', and 'strand' information correctly o readAligned MAQMapview failed for most chromosome labels CHANGES IN VERSION 1.0 ---------------------- SIGNIFICANT USER-VISIBLE CHANGES o SRFilter allows construction of filters that can be used to subset existing data objects, or filter incoming (readAligned, at the moment) objects. o readAligned for Solexa-based alignments return 'strand' information as factor with levels "-", "+", "*" (strand not relevant), NA (no strand information available). o srorder, srsort, srrank, and srduplicated for AligendRead class now sort based on chromosome, strand, position AND sread; previous behavior can be recovers by extracting the sequences srsort(sread(aln)), etc. o Functions using SolexaPath now search all relevant directories, e.g., in analysisPath, rather than the first BUG FIXES o 'run' in eland_export files is correctly parsed as a factor (start date: 29 September, 2008)