CHANGES IN VERSION 1.64
-----------------------
BUG FIXES
o (v 163.1) rely on system-provided zlib on all platforms
CHANGES IN VERSION 1.58
-----------------------
BUG FIXES
o (v 1.57.1, 1.56.1) avoid integer overflow in countFastq()
https://github.com/Bioconductor/ShortRead/issues/10
CHANGES IN VERSION 1.50
-----------------------
NEW FEATURES
o (v 1.49.1) `as(., "QualityScaledDNAStringSet")` propagates
names. See https://github.com/Bioconductor/ShortRead/issues/3.
o (v 1.49.1) implement`as(., "DNAStringSet")`. See
https://github.com/Bioconductor/ShortRead/issues/3.
BUG FIXES
o (v 1.49.3) report invalid FastqStreamer / FastqSampler on
re-serialized objects. Fixes
https://github.com/Bioconductor/ShortRead/issues/5.
CHANGES IN VERSION 1.48
-----------------------
NEW FEATURES
o (v 1.47.1) `countFastq()` counts the number of records,
nucleotides, and quality scores in one or several fastq files.
CHANGES IN VERSION 1.44
-----------------------
BUG FIXES
o (v 1.44.2) readFastq argument qualityType = "Auto" correctly
identifies SFastqQuality. See
https://github.com/Bioconductor/ShortRead/pull/2
CHANGES IN VERSION 1.37
-----------------------
BUG FIXES
o (v. 1.37.2) FastqQuality() includes the last printable ASCII
character '~'
o (v. 1.37.3) countLines() returns numeric values, to allow for
files with more than 2^31-1 lines
CHANGES IN VERSION 1.35
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Reads up to 2M bases can be parsed
CHANGES IN VERSION 1.27
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o fastqFilter allows several input 'files' to be written to a
single 'destinations'.
o readAligned() for BAM files is defunct. QA and associated
methods removed.
o srapply removed
o 'legacy' function readInfo() renamed readIntensityInfo()
CHANGES IN VERSION 1.25
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o srapply is defunct
o readAligned() for BAM files is deprecated; use
GenomicAlignments::readGAligned instead.
BUG FIXES
o close opened files when parsing old bowtie, soap, and solexa
export file formats.
o Don't allow R memory to be released prematurely when processing
old bowtie file formats / creating external pointers.
o writeFastq,FastqFile obeys 'compress' argument; mode must be
specified by the caller (typically mode="a")
CHANGES IN VERSION 1.23
-----------------------
NEW FEATURES
o alphabetScore,PhredQuality-method implemented
o reverse, reverseComplement methods for ShortReadQ objects
o srlist, to access SRList data as a base R list.
SIGNIFICANT USER-VISIBLE CHANGES
o readFastq qualityType="Auto" chooses base-64 encoding when no
characters are encoded at less than 59, and some are encoded at
greater than 74.
BUG FIXES
o report() prints adapter contaminants correctly when user has
stringsAsFactors=FALSE
o qa(..., sample=FALSE) no longer tries to re-match 'pattern'
argument
CHANGES IN VERSION 1.21
-----------------------
NEW FEATURES
o writeFastq can write (and does so by default) gz-compressed files
SIGNIFICANT USER-VISIBLE CHANGES
o Use BiocParallel rather than srapply, mark srapply as 'Deprecated'
o qa,character-method defaults to type="fastq"
o Input of 'legacy' formats marked as such
o alphabetByCycle supports amino acid string sets
CHANGES IN VERSION 1.19
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o qa(..., type="fastq") uses a sample of n=1000000 reads by
default, rather than then entire file; use sample=FALSE to
revert to previous behavior.
NEW FEATURES
o encoding,FastqQuality and encoding,SFastqQuality provide a
convenient map between letter encodings and their corresponding
integer quality values.
o filterFastq transforms one fastq file to another, removing reads
or nucleotides via a user-specified
function. trimEnds,character-method & friends use this for an
easy way to remove low-quality base.
BUG FIXES
o writeFastq successfully writes zero-length fastq files.
o FastqStreamer / FastqSampler warn on incomplete (corrupt) files
CHANGES IN VERSION 1.17
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o FastqSampler can return records in the order encountered in the
sampled file.
o Increase to 10000 the number of reads examined for determining
Fastq quality type
o as(FastqQuality, "numeric") returns a vector of quality scores
concatenated end to end (previously cycle to cycle), without
padding to effective equal width
BUG FIXES
o trimTails, successive=TRUE would return inconsistent results
o FastqStreamer, FastqSampler parse fastq files created with '\r'
CHANGES IN VERSION 1.15
-----------------------
NEW FEATURES
o FastqStreamer accepts IRanges for selecting input records
SIGNIFICANT USER-VISIBLE CHANGES
o as(ShortReadQ, "matrix") now accepts ShortReadQ instances with
heterogeneous widths, returning a matrix x[i, j] with NA values in
when j > width()[i].
BUG FIXES
o readAligned, type="BAM" correctly adds required 'what' elements
o FastqSampler would only randomize first read; introduced 1.13.9
2011-12-02, fixed 1.15.4 2012-04-25
o report(qa, ...) no longer produces obviously confused base
calls per cycle
o FastqFileList would fail to initialize correctly from a
character vector
CHANGES IN VERSION 1.13
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o FastqSampler is considerably faster
o FastqSampler and FastqStreamer require explicit close() to avoid
warnings about closing unused connections
BUG FIXES
o qa reports on very large lanes would overflow alphabetFrequency
o qa report scales adapaterContamination correctly
o FastqSampler would rarely sample fewer than requested reads
o FastqSampler supports outputs of >2^31 - 1 total nucleotides
o readFastq parses records with 0 width
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
information
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)