CHANGES IN VERSION 1.36.3
-------------------------
BUG FIXES
o `seqSetFilter(, action="intersect", ret.idx=TRUE)`, see
https://github.com/zhengxwen/SeqArray/issues/80
CHANGES IN VERSION 1.36.2
-------------------------
BUG FIXES
o fix the bug at multi-allelic sites with more than 15 different alleles,
see https://github.com/zhengxwen/SeqArray/issues/78
CHANGES IN VERSION 1.36.1
-------------------------
UTILITIES
o new option 'ext_nbyte' in seqGet2bGeno()
BUG FIXES
o `seqExport()` failed when there is no variant
o `seqSetFilter(, ret.idx=TRUE)`, see
https://github.com/zhengxwen/SeqArray/issues/80
CHANGES IN VERSION 1.36.0
-------------------------
NEW FEATURES
o new functions `seqUnitCreate()`, `seqUnitSubset()` and `seqUnitMerge()`
o new functions `seqFilterPush()` and `seqFilterPop()`
o new functions `seqGet2bGeno()` and `seqGetAF_AC_Missing()`
o new function `seqGetData(, "$dosage_sp")` for a sparse matrix of dosages
o the first argument 'gdsfile' can be a file name in `seqAlleleFreq()`,
`seqAlleleCount()`, `seqMissing()`
o new function `seqMulticoreSetup()` for setting a multicore cluster
according to a numeric value assigned to the argument 'parallel'
UTILITIES
o allow opening a duplicated GDS file ('allow.duplicate=TRUE') when the
input is a file name instead of a GDS object in `seqGDS2VCF()`,
`seqGDS2SNP()`, `seqGDS2BED()`, `seqVCF2GDS()`, `seqSummary()`,
`seqCheck()` and `seqMerge()`
o remove the deprecated '.progress' in `seqMissing()`, `seqAlleleCount()`
and `seqAlleleFreq()`
o add `summary.SeqUnitListClass()`
o no genotype and phase data nodes from `seqSNP2GDS()` if SNP dosage GDS
is the input
BUG FIXES
o `seqUnitApply()` works correctly with selected samples if 'parallel' is
a non-fork cluster
o `seqVCF2GDS()` and `seqVCF_Header()` work correctly if the VCF header has
white space
o `seqGDS2BED()` with selected samples for sex and phenotype information
o `seqGDS2VCF()` failed if there is no 'genotype/data' in the GDS file
CHANGES IN VERSION 1.32.0
-------------------------
NEW FEATURES
o new option 'ret.idx' in `seqSetFilter()` for unsorted sample and variant
indices
o new option 'ret.idx' in `seqSetFilterAnnotID()` for unsorted variant
index
o rewrite the function `seqSetFilterPos()`: new options 'ref' and 'alt',
'multi.pos=TRUE' by default
o new option 'packed.idx' in `seqAddValue()` for packing an indexing
variable
o new option 'warn' in `seqSetFilter()` to enable or disable the warning
o new functions `seqNewVarData()` and `seqListVarData()` for
variable-length data
UTILITIES
o allow no variant in `seqApply()` and `seqBlockApply()`
o the list object returned from `seqGetData()` always have names if there
are more than one input variable names
BUG FIXES
o `seqGDS2VCF()` should output "." instead of NA in the FILTER column
o `seqGetData()` should support factor when '.padNA=TRUE' or '.tolist=TRUE'
o fix `seqGDS2VCF()` with factor variables
o `seqSummary(gds, "$filter")` should return a data frame with zero row if
'annotation/filter' is not a factor
CHANGES IN VERSION 1.30.0
-------------------------
UTILITIES
o show a warning when an unsorted index is used in `seqSetFilter()`
o show a message if `seqVCF_Header()` fails
o a new option 'chr_prefix' in `seqGDS2VCF()`
BUG FIXES
o `seqVCF_Header()` fixes 'contig' in the header of VCF if there are
different fields
CHANGES IN VERSION 1.28.1
-------------------------
BUG FIXES
o `seqRecompress(, verbose=FALSE)` works correctly
o `seqSetFilter(, action="push+set")` should not reset the filter
before setting a new filter
CHANGES IN VERSION 1.28.0
-------------------------
NEW FEATURES
o new functions `seqUnitSlidingWindows()`, `seqUnitApply()`,
`seqUnitFilterCond()`
o new variable "$variant_index", "$sample_index" in `SeqGetData()`,
`seqBlockApply()` and `seqUnitApply()` to get the indices of selected
variants
o new arguments '.padNA' and '.envir' in `seqGetData()`
o new functions `seqSetFilterAnnotID()` and `seqGDS2BED()`
o multicore function in `seqBED2GDS(, parallel=)`
o new package-wide option `options(seqarray.nofork=TRUE)` to disable forking
o new option 'minor' in `seqAlleleFreq()` and `seqAlleleCount()`
o new option 'verbose' in `seqMissing()`, `seqAlleleFreq()` and
`seqAlleleCount()`; '.progress' is deprecated, but still can be used
for compatiblity
o `seqAlleleFreq()`, `seqAlleleCount()`, `seqMissing()`,
`seqSetFilterCond()` work on 'annotation/format/DS', if 'genotype/data'
is not available
UTILITIES
o `seqAddValue()` adds vectors, matrices and data frame to "annotation/info"
o `seqBED2GDS()` allows a single file name without the extended file names
(.bed, .fam, .bim)
o allele flip in `seqBED2GDS()` to allow major allele to be reference
o rewrite `seqGetData()` for faster loading
o significantly improve `seqBlockApply()` on 'annotation/info/VARIABLE'
(https://github.com/zhengxwen/SeqArray/issues/59)
o add a S3 method `print.SeqVCFHeaderClass()` for `seqVCF_Header()`
o new option '.tolist' in `seqGetData()`, `seqBlockApply()` and
`seqUnitApply()`
o String "." in a VCF file are converted to a blank string (missing value)
in `seqVCF2GDS()`
o add a class name 'SeqVarDataList' to the returned 'list(length, data)'
from `seqGetData()`
o new option `seqMissing(, per.variant=NA)`
o add `comment.char=""` to `seqBED2GDS()`
CHANGES IN VERSION 1.26.2
-------------------------
NEW FEATURES
o multiple variable names are allowed in `seqGetData(, var.name=)`
BUG FIXES
o fix `seqGetData(, "genotype", .useraw=NA)`
(https://github.com/zhengxwen/SeqArray/issues/58)
CHANGES IN VERSION 1.26.1
-------------------------
BUG FIXES
o fails to correctly select duplicate indices in
`seqSetFilter(f, variant.sel=)`
CHANGES IN VERSION 1.26.0
-------------------------
NEW FEATURES
o new function `seqAddValue()`
UTILITIES
o RLE chromosome coding in `seqBED2GDS()`
o change the file name "vignettes/R_Integration.Rmd" to
"vignettes/SeqArray.Rmd", so `vignette("SeqArray")` can work directly
o correct Estimated remaining Time to Complete (ETC) for load balancing in
`seqParallel()`
BUG FIXES
o `seqBED2GDS(, verbose=FALSE)` should have no display
CHANGES
o use a svg file instead of png in vignettes
CHANGES IN VERSION 1.24.2
-------------------------
NEW FEATURES
o add the compiler information in `seqSystem()`
o new arguments '.balancing', '.bl_size' and '.bl_progress' in
`seqParallel()` for load balancing
UTILITIES
o improve unix forking processes for load balancing in `seqParallel()`
BUG FIXES
o fix `seqSummary()` when no phase data
CHANGES IN VERSION 1.24.0
-------------------------
NEW FEATURES
o a new function `seqResetVariantID()`
o a new option in `seqRecompress(, compress="none")` to uncompress all data
o `seqGetData()` allows a GDS file name in the first argument
CHANGES IN VERSION 1.22.6
-------------------------
BUG FIXES
o `seqSetFilter(, sample.id=)` fails to correctly select samples in a few
cases (since SeqArray>=v1.22.0 uses the distribution of selected samples
to optimize the data access of genotypes, see
https://github.com/zhengxwen/SeqArray/issues/48)
o the bgzf VCF file is truncated in `seqGDS2VCF()` since the file is not
closed appropriately
o invalid chromosomes and position in the output of `seqMerge()` when
merging different samples but same variants
CHANGES IN VERSION 1.22.3
-------------------------
NEW FEATURES
o a new option 'scenario' in `seqVCF2GDS()` and `seqBCF2GDS()`
UTILITIES
o more information in `seqDelete()`
BUG FIXES
o export a haploid VCF file using `seqGDS2VCF()`
o export VCF without any FORMAT data in `seqGDS2VCF()`
o export GDS without genotypes in `seqExport()`
o fix parallel file writing in seqVCF2GDS(), when no genotype
CHANGES IN VERSION 1.22.0
-------------------------
NEW FEATURES
o `seqSNP2GDS()` imports dosage GDS files
o `seqVCF_Header()` allows a BCF file as an input
o a new function `seqRecompress()`
o a new function `seqCheck()` for checking the data integrity of a SeqArray
GDS file
o `seqGDS2SNP()` exports dosage GDS files
UTILITIES
o avoid duplicated meta-information lines in `seqVCF2GDS()` and
`seqVCF_Header()`
o require >= R_v3.5.0, since reading from connections in text mode is
buffered
o `seqDigest()` requires the digest package
o optimization in reading genotypes from a subset of samples (according to
gdsfmt_1.17.5)
BUG FIXES
o `seqVCF2GDS()` and `seqVCF_Header()` are able to import site-only VCF
files (i.e., VCF with no sample)
o fix `seqVCF2GDS()` and `seqBCF2GDS()` since reading from connections in
text mode is buffered in R >= v3.5.0
CHANGES IN VERSION 1.20.1
-------------------------
BUG FIXES
o `seqExport()` fails to export haploid data (e.g., Y chromosome)
o `seqVCF2GDS()` fails to convert INFO variables when Number="R"
CHANGES IN VERSION 1.20.0
-------------------------
NEW FEATURES
o `seqGDS2VCF()` outputs a bgzip vcf file for tabix indexing
o two more options "Ultra" and "UltraMax" in `seqStorageOption()`
o '@chrom_rle_val' and '@chrom_rle_len' are added to a GDS file for
faster chromosome indexing
o new function `seqBCF2GDS()` (requiring the software bcftools)
o new function `seqSetFilterPos()`
o new variable "$dosage_alt" in `seqGetData()` and `seqApply()`
o import VCF files with no GT in `seqVCF2GDS()`
UTILITIES
o `seqDigest(f, "annotation/filter")` works on a factor variable
o improve the computational efficiency of `seqMerge()` to avoid genotype
recompression by padding the 2-bit genotype array in bytes
o significantly improve `seqBlockApply()` (its speed is close to
`seqApply()`)
o reduce the overhead in `seqSetFilter(, variant.sel=...)`
CHANGES IN VERSION 1.18.2
-------------------------
BUG FIXES
o fix an issue: `seqSetFilterChrom()` extends a genomic range
upstream and downstream 1bp
o use `.onLoad()` instead of `.onAttach()` to fix
https://support.bioconductor.org/p/104405/#104443
CHANGES IN VERSION 1.18.0
-------------------------
NEW FEATURES
o progress information: showing overall running time when completed
o new variable names "$ref" and "$alt" can be used in `seqGetData()` and
`seqBlockApply()`
o new argument '.progress' in `seqDigest()`
o new argument 'ref.allele' in `seqAlleleCount()`
o new variable name "$chrom_pos_allele" can be used in `seqGetData()` and
`seqBlockApply()`
UTILITIES
o move VariantAnnotation to the suggest field from the import field
o remove an unused argument '.list_dup' in `seqBlockApply()`
o slightly improve the computational efficiency of `seqAlleleFreq()` and
`seqAlleleCount()` when 'ref.allele=0'
o `seqGetData(f, "$chrom_pos")` outputs characters with the format
'chromosome:position' instead of 'chromosome_position'
BUG FIXES
o fix the unexpected behaviors in `seqSetFilter(, action="push")` and
`seqSetFilter(, action="push+intersect")`
o fix a bug in `seqGetData(f, "$dosage")` when the number of unique alleles
at a site greater than 3 (https://github.com/zhengxwen/SeqArray/issues/21)
o fix a bug in `seqSNP2GDS()` for inverted genotypes during importing data
from SNP GDS files (https://github.com/zhengxwen/SeqArray/issues/22)
o fix an issue of no phase data in `seqExport()`
CHANGES IN VERSION 1.16.0
-------------------------
o a new argument 'intersect' in `seqSetFilter()` and `seqSetFilterChrom()`
o a new function `seqSetFilterCond()`
o `seqVCF2GDS()` allows arbitrary numbers of different alleles if REF and
ALT in VCF are missing
o optimize internal indexing for FORMAT annotations to avoid reloading
the indexing from the GDS file
o a new CITATION file
o 'LZMA_RA' is the default compression method in `seqBED2GDS()` and
`seqSNP2GDS()`
o `seqVCF_Header()` correctly calculates ploidy with missing genotypes
CHANGES IN VERSION 1.14.1
-------------------------
o The default compression setting in `seqVCF2GDS()` and `seqMerge()` is
changed from "ZIP_RA" to "LZMA_RA"
o `seqVCF2GDS()`: variable-length encoding method is used to store
integers in the FORMAT field of VCF files to reduce the file size and
compression time
CHANGES IN VERSION 1.12.9
-------------------------
o the version number was bumped for the Bioconductor release version 3.3
o `seqVCF_SampID()`, `seqVCF_Header()` and `seqVCF2GDS()` allow a
connection object instead of a file name
o "$num_allele" is allowed in `seqGetData()` and `seqApply()` (the numbers
of distinct alleles)
o a new option '.progress' in `seqAlleleFreq()`, `seqMissing()` and
`seqAlleleCount()`
o 'as.is' can be a `gdsn.class` object in `seqApply()`
o v1.12.7: a new argument 'parallel' in `seqApply()`, BiocParallel
integration in `seqParallel()` and a new function `seqBlockApply()`
o v1.12.8: a new function `seqGetParallel()`
CHANGES IN VERSION 1.12.0
-------------------------
o utilizes the official C API `R_GetConnection()` to accelerate text
import and export, requiring R (>=v3.3.0); alternative version (backward
compatible with R_v2.15.0) is also available on github
(https://github.com/zhengxwen/SeqArray/releases/tag/v1.11.18)
o ~4x speedup in the sequential version of `seqVCF2GDS()`, and
`seqVCF2GDS()` can run in parallel
o variables in "annotation/format/" should be two-dimensional as what
mentioned in the vignette.
o rewrite `seqSummary()`
o a new vignette file with Rmarkdown format (replacing SeqArray-JSM2013.pdf)
o bug fix in `seqBED2GDS()` if the total number of genotypes > 2^31
(integer overflow)
o bug fixes in `seqMerge()` if chromosome and positions are not unique
o `seqStorage.Option()` is renamed to `seqStorageOption()`
o new function `seqDigest()`
o `seqVCF.Header()` is renamed to `seqVCF_Header()`,
`seqVCF.SampID()` is renamed to `seqVCF_SampID()`
o seqSetFilter(): 'samp.sel' is deprecated since v1.11.12, please use
'sample.sel' instead
o accelerate reading genotypes with SSE2(+13%) and AVX2(+23%)
o new function `seqSystem()`
o allow "$dosage" in `seqGetData()` and `seqApply()` for the dosages of
reference allele
o accelerate `seqSetFilterChrom()` and allow a selection with
multiple regions
o new methods `\S4method{seqSetFilter}{SeqVarGDSClass, GRanges}()` and
`\S4method{seqSetFilter}{SeqVarGDSClass, GRangesList}()`
o 'as.is' in `seqApply()` allows a 'connection' object (created by file,
gzfile, etc)
o `seqSummary(f, "genotype")$seldim` returns a vector with 3 integers
(ploidy, # of selected samples, # of selected variants) instead of
2 integers
CHANGES IN VERSION 1.10.6
-------------------------
o fix a memory issue in `seqAlleleFreq()` when 'ref.allele' is a vector
o `seqSetFilter()` allows numeric vectors in 'samp.sel' and 'variant.sel'
o `seqSummary()` returns ploidy and reference
o `seqStorage.Option()` controls the compression level of FORMAT/DATA
o `seqVCF2GDS()` allows extract part of VCF files via 'start' and 'count'
o `seqMerge()` combines multiple GDS files with the same samples
o export methods for compatibility with VariantAnnotation
o a new argument '.useraw' in `seqGetFilter()`
o a new argument 'allow.duplicate' in `seqOpen()`
o fix a bug in `seqParallel()`
(https://github.com/zhengxwen/SeqArray/issues/11) and optimize
its performance
o 'gdsfile' could be NULL in `seqParallel()`
CHANGES IN VERSION 1.10.0
-------------------------
o a new function `seqGDS2SNP()`
o supported by the SNPRelate package
o support `seqApply(..., margin="by.sample")`
o new functions `seqOptimize()`, `seqMissing()`, `seqAlleleFreq()`,
`seqNumAllele()` and `seqSetFilterChrom()`
o "intersection" and "push+intersection" in `seqSetFilter()`
o parallel implementation in `seqNumAllele()`, `seqMissing()` and
`seqAlleleFreq()`
o a new function `seqExport()`
o new argument ".useraw" in `seqApply()`
o fix a bug for duplicated "variant.id",
https://github.com/zhengxwen/SeqArray/issues/7
o fix an issue of `seqVCF2GDS()` when there are duplicated format or
info ID
o improve access speed (+50%, benchmark on calling
seqApply(..., FUN=function(x) {}))
o new functions `seqSNP2GDS()`, `seqBED2GDS()`, `seqAlleleCount()` and
`seqResetFilter()`
o `seqCompress.Option()` is renamed to `seqStorage.Option()`
o "ZIP_RA" is the default value in `seqStorageOption()` and other
functions instead of "ZIP_RA.max"
o `seqSetFilter()` becomes a S4 method
CHANGES IN VERSION 1.8.0
-------------------------
o bug fix in getting genotypes if position > 2^31
o add an option 'ignore.chr.prefix' to the function `seqVCF2GDS()`
o `seqVCF2GDS()` ignores the INFO or FORMAT variables if they are not
defined ahead
o a new action 'push+set' in the function `seqSetFilter()`
o bug fix if 'requireNamespace("SeqArray")' is called from other packages
CHANGES IN VERSION 1.6.0
-------------------------
o fix a bug in `seqVCF2GDS()` when the values in the FILTER column are
all missing
o enhance `seqVCF.Header()`
o support the LinkingTo mechanism
o fix the error in haploid genotypes (Y chromosome)
CHANGES IN VERSION 1.4.0
-------------------------
o update according to the new version of VariantAnnotation
o update test codes to avoid the conflict
o bumped version as all packages that depend on Rcpp must be rebuilt
o modify to new biocViews to DESCRIPTION file
CHANGES IN VERSION 1.2.0
-------------------------
o add a new argument "action" to the function `seqSetFilter()`
o add a new function 'seqInfoNewVar' which allows adding new variables
to the INFO fields
o minor bug fix in asVCF
o update man page "SeqVarGDSClass-class.Rd" with new methods
o in DESCRIPTION, BiocGenerics listed in "Suggests" instead of "Imports"
as suggested by R CMD check
o bug fix in seqDelete
o revise the function 'seqTranspose' according to the update of
gdsfmt (v1.0.0)
o revise the argument 'var.index' in the function `seqApply()`
o basic supports of 'GRanges' and 'DNAStringSetList'
o added methods 'qual', 'filt', 'asVCF'
o 'granges' method uses length of reference allele to set width
o minor bug fix to avoid `seqGetData()` crashing when no value returned
from a variable-length variable
o update documents
CHANGES IN VERSION 1.0.0
-------------------------
o the version number was bumped for the Bioconductor release version
CHANGES IN VERSION 0.99.0
-------------------------
o initial Bioconductor package submission