NEWS

ShortRead 1.58

BUG FIXES

(v 1.57.1, 1.56.1) avoid integer overflow in countFastq() https://github.com/Bioconductor/ShortRead/issues/10

ShortRead 1.50

NEW FEATURES

(v 1.49.1) 'as(., "QualityScaledDNAStringSet")' propagates names. See https://github.com/Bioconductor/ShortRead/issues/3.
(v 1.49.1) implement'as(., "DNAStringSet")'. See https://github.com/Bioconductor/ShortRead/issues/3.

BUG FIXES

(v 1.49.3) report invalid FastqStreamer / FastqSampler on re-serialized objects. Fixes https://github.com/Bioconductor/ShortRead/issues/5.

ShortRead 1.48

NEW FEATURES

(v 1.47.1) 'countFastq()' counts the number of records, nucleotides, and quality scores in one or several fastq files.

ShortRead 1.44

BUG FIXES

(v 1.44.2) readFastq argument qualityType = "Auto" correctly identifies SFastqQuality. See https://github.com/Bioconductor/ShortRead/pull/2

ShortRead 1.37

BUG FIXES

(v. 1.37.2) FastqQuality() includes the last printable ASCII character '~'
(v. 1.37.3) countLines() returns numeric values, to allow for files with more than 2^31-1 lines

ShortRead 1.35

SIGNIFICANT USER-VISIBLE CHANGES

Reads up to 2M bases can be parsed

ShortRead 1.27

SIGNIFICANT USER-VISIBLE CHANGES

fastqFilter allows several input 'files' to be written to a single 'destinations'.
readAligned() for BAM files is defunct. QA and associated methods removed.
srapply removed
'legacy' function readInfo() renamed readIntensityInfo()

ShortRead 1.25

SIGNIFICANT USER-VISIBLE CHANGES

srapply is defunct
readAligned() for BAM files is deprecated; use GenomicAlignments::readGAligned instead.

BUG FIXES

close opened files when parsing old bowtie, soap, and solexa export file formats.
Don't allow R memory to be released prematurely when processing old bowtie file formats / creating external pointers.
writeFastq,FastqFile obeys 'compress' argument; mode must be specified by the caller (typically mode="a")

ShortRead 1.23

NEW FEATURES

alphabetScore,PhredQuality-method implemented
reverse, reverseComplement methods for ShortReadQ objects
srlist, to access SRList data as a base R list.

SIGNIFICANT USER-VISIBLE CHANGES

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

report() prints adapter contaminants correctly when user has stringsAsFactors=FALSE
qa(..., sample=FALSE) no longer tries to re-match 'pattern' argument

ShortRead 1.21

NEW FEATURES

writeFastq can write (and does so by default) gz-compressed files

SIGNIFICANT USER-VISIBLE CHANGES

Use BiocParallel rather than srapply, mark srapply as 'Deprecated'
qa,character-method defaults to type="fastq"
Input of 'legacy' formats marked as such
alphabetByCycle supports amino acid string sets

ShortRead 1.19

SIGNIFICANT USER-VISIBLE CHANGES

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

encoding,FastqQuality and encoding,SFastqQuality provide a convenient map between letter encodings and their corresponding integer quality values.
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

writeFastq successfully writes zero-length fastq files.
FastqStreamer / FastqSampler warn on incomplete (corrupt) files

ShortRead 1.17

SIGNIFICANT USER-VISIBLE CHANGES

FastqSampler can return records in the order encountered in the sampled file.
Increase to 10000 the number of reads examined for determining Fastq quality type
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

trimTails, successive=TRUE would return inconsistent results
FastqStreamer, FastqSampler parse fastq files created with '\r'

ShortRead 1.15

NEW FEATURES

FastqStreamer accepts IRanges for selecting input records

SIGNIFICANT USER-VISIBLE CHANGES

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

readAligned, type="BAM" correctly adds required 'what' elements
FastqSampler would only randomize first read; introduced 1.13.9 2011-12-02, fixed 1.15.4 2012-04-25
report(qa, ...) no longer produces obviously confused base calls per cycle
FastqFileList would fail to initialize correctly from a character vector

ShortRead 1.13

SIGNIFICANT USER-VISIBLE CHANGES

FastqSampler is considerably faster
FastqSampler and FastqStreamer require explicit close() to avoid warnings about closing unused connections

BUG FIXES

qa reports on very large lanes would overflow alphabetFrequency
qa report scales adapaterContamination correctly
FastqSampler would rarely sample fewer than requested reads
FastqSampler supports outputs of >2^31 - 1 total nucleotides
readFastq parses records with 0 width

ShortRead 1.11

NEW FEATURES

trimTails to trim low quality trailing nucleotides
trimEnds to remove arbitrary (vectors of) letters from reads or qualities
FastqStreamer to iterate over a fastq file
FastqFile, FastqFileList to represent fastq files

SIGNIFICANT USER-VISIBLE CHANGES

writeFastq has argument full, default value FALSE, disabling printing of identifier a second time in '+' line
srapply requires that options(srapply_fapply="parallel") or options(srapply_fapply="Rmpi") to enable parallel processing via fapply

BUG FIXES

SolexaRealign, SolexaAlign, and SolexaResult transposed strand information
FastqSampler segfaulted on some files
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.

ShortRead 1.9

NEW FEATURES

Support for HiSeq tile layout
Track reads passing filters, including across logical filter operations

ShortRead 1.7

BUG FIXES

qa() represented the per-cycle quality scores incorrectly; this influenced qa[["perCycle"]][["quality"]][["Score"]], but not the qa report.
qa() for type="SolexaExport" transposed the 'aligned' and 'filtered' labels on all elements of SolexaExportQA. Thanks Nicolas Delhomme for the report.
report() failed when each read was unique. Thanks Peng Yu for the report.

SIGNIFICANT USER-VISIBLE CHANGES

The perCycleQuality graph in the qa report now includes boxplots for all cycles instead of just the median value.
A depthOfCoverage graph has been added to the qa report for BAM, Bowtie, SolexaExport and SolexaRealign file types.
An adapterContamination measure has been added to the qa report for BAM, Bowtie, SolexaExport, SolexaRealign and Fastq file types.
srorder is now stable (the original order of identical is preservered).

NEW FEATURES

Add class BAMQA. qa() can now be called on BAM files.
The param argument in readAligned() and qa() for type="BAM" can now be a single ScanBamParam object or a list of them.
FastqSampler can be used to draw samples from a fastq file.

ShortRead 1.5

SIGNIFICANT USER-VISIBLE CHANGES

levels(strand(aln)) is c("+", "-", "*") (was c("-", "+", "*"))
Add USE.NAMES argument to srapply, minimum length to (internal) function ..reduce.

NEW FEATURES

Optionally retrieve multiplex bar code, paired read number, and id from SolexaExport (contribution from Nicolas Delhomme)
renew() and renewable() provide an interface to updating ShortRead instances
srapply checks for and uses multicore
readIntensities supports Illumina RTA '.cif' / '.cnf' files
readAligned type="BAM" parses BAM files, extracting simple (no indel) cigars

BUG FIXES

readIntensities type="IparIntensity" correctly handles multiple tiles

ShortRead 1.3

SIGNIFICANT USER-VISIBLE CHANGES

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).
readAligned,character-method, type="Bowtie" and readFastq return FastqQuality by default.
coverage,AlignedRead-method now returns an RleList

NEW FEATURES

qa reports from _realign.txt, MAQMap files
QualityScoreDNAStringSet coercion methods
qa type="character" now accepts a filter argument with value srFilter()
alphabetByCycle supports variable-width XStringSets
qa,ShortReadQ and qa,list methods for qa on existing objects

BUG FIXES

Parse .gz realign files
alphabetScore,FastqQuality-method shifted quality by +1

ShortRead 1.1

SIGNIFICANT USER-VISIBLE CHANGES

454 quality scores are returned as FastqQuality-encoded
For functions accepting dirPath, pattern to name files, allow dirPath to be a vector of file names when pattern is character().
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

Add Bowtie as a 'type' value for qa and report
Add dustyScore() and dustyFilter() to identify low-complexity regions
Parse _qseq files (to ShortReadQ or XDataFrame)
Parse IPAR image intensity files _int.txt.p, _nse.txt.p, _pos.txt
Create HTML-based quality assessment reports
Add trimLRPatterns() for ShortRead and derived classes (ShortReadQ, AlignedRead).
Add narrow() for ShortRead, QualityScore, and derived classes.
Use append() to append two objects of the same ShortReadQ or QualityScore and derived classes together
writeFastq for classes derived from ShortReadQ
Input functions support .gz or text files.
readIntensity reads Solexa image intensity files into R, including information about lane, tile, x, and y coordinates of each read.
readPrb returns different types of objects, depending on the 'as' argument of the readPrb,character-method.
readXStringSet gets arguments skip, nrows; argument order changed slightly
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.
readAligned gains a Solexa _results parser (_results files are listed as 'intermediate' in the Solexa manual, and not a good end-point for analysis)
readAligned gains a Bowtie output parser
readAligned gains ability to parse MAQ 0.7 version binary files

BUG FIXES

readQual would fail to read 454 quality scores correctly when these spanned more than one line of input per read
coverage treated reads as 1 base longer than they were
FastqQuality got the quality encoding off by one in as(x, "matrix")
qa_solexa.Rnw incorrectly displayed read occurences when lanes were presented out-of-order (an unusual occurence)
readAligned SolexaAlign, etc., updated to parse 'chromsome' and 'position', and 'strand' information correctly
readAligned MAQMapview failed for most chromosome labels

ShortRead 1.0

SIGNIFICANT USER-VISIBLE CHANGES

SRFilter allows construction of filters that can be used to subset existing data objects, or filter incoming (readAligned, at the moment) objects.
readAligned for Solexa-based alignments return 'strand' information as factor with levels "-", "+", "*" (strand not relevant), NA (no strand information available).
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.
Functions using SolexaPath now search all relevant directories, e.g., in analysisPath, rather than the first

BUG FIXES

'run' in eland_export files is correctly parsed as a factor (start date: 29 September, 2008)