NEWS

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SeqArray 1.44.0

UTILITIES

• tweak the display of progress information in 'seqVCF2GDS()'
• 'seqVCF_Header(, getnum=TRUE, verbose=TRUE)' to show the progress information for scanning the VCF file
• new 'seqGetData(, "$dosage_alt2")' and 'seqGetData(, "$dosage_sp2")' for sex chromosomes, when the alleles are partially missing (e.g., genotypes on chromosome X for males)
• new 'verbose.clean' in 'seqExport()' to control how much information to be displayed

SeqArray 1.42.4

BUG FIXES

• 'seqGetData(, "$dosage_alt")' and 'seqGetData(, "$dosage_sp")' work correctly when the ploidy is >2 and there are missing alleles
• fix a bug that ‘seqParallel()' does not call a user-defined ’.combine' when 'parallel=1'

SeqArray 1.42.1

UTILITIES

• update the help files of 'seqBlockApply()' and 'seqUnitApply()'
• detect the output filename extension in 'seqGDS2VCF()' without considering the case of the characters, supporting .gz, .bgz, .bz and .xz as a filename extension
• fix the compiler warning: -Wformat-security
• new option 'include.pheno=TRUE' in 'seqBED2GDS()'

SeqArray 1.42.0

UTILITIES

• new option 'write.rsid' in 'seqGDS2BED()'

SeqArray 1.40.1

BUG FIXES

• 'seqAddValue(gdsfile, varnm="position")' works correctly

SeqArray 1.40.0

• fix the compiler warning: sprintf is deprecated

SeqArray 1.38.0

UTILITIES

• new option 'ext_nbyte' in 'seqGet2bGeno()'
• 'seqAlleleCount()' and 'seqGetAF_AC_Missing()' return NA instead of zero when all genotypes are missing at a site
• 'seqGDS2VCF()' does not output the FORMAT column if there is no selected sample (e.g., site-only VCF files)
• 'seqGetData(, "$chrom_pos2")' is similar to 'seqGetData(, "$chrom_pos")' except the duplicates with the suffix ("_1", "_2" or >2)

NEW FEATURES

• 'seqGDS2BED()' can convert to PLINK BED files with the best-guess genotypes when there are only numeric dosages in the GDS file
• 'seqEmptyFile()' outputs an empty GDS file

SeqArray 1.36.2

BUG FIXES

• fix the bug at multi-allelic sites with more than 15 different alleles, see https://github.com/zhengxwen/SeqArray/issues/78

SeqArray 1.36.1

BUG FIXES

• 'seqExport()' failed when there is no variant
• 'seqSetFilter(, ret.idx=TRUE)', see https://github.com/zhengxwen/SeqArray/issues/80

SeqArray 1.36.0

NEW FEATURES

• new functions 'seqUnitCreate()', 'seqUnitSubset()' and 'seqUnitMerge()'
• new functions 'seqFilterPush()' and 'seqFilterPop()'
• new functions 'seqGet2bGeno()' and 'seqGetAF_AC_Missing()'
• new function 'seqGetData(, "$dosage_sp")' for a sparse matrix of dosages
• the first argument 'gdsfile' can be a file name in 'seqAlleleFreq()', 'seqAlleleCount()', 'seqMissing()'
• new function ‘seqMulticoreSetup()' for setting a multicore cluster according to a numeric value assigned to the argument ’parallel'

UTILITIES

• 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()'
• remove the deprecated '.progress' in 'seqMissing()', 'seqAlleleCount()' and 'seqAlleleFreq()'
• add 'summary.SeqUnitListClass()'
• no genotype and phase data nodes from 'seqSNP2GDS()' if SNP dosage GDS is the input

BUG FIXES

• ‘seqUnitApply()' works correctly with selected samples if ’parallel' is a non-fork cluster
• 'seqVCF2GDS()' and 'seqVCF_Header()' work correctly if the VCF header has white space
• 'seqGDS2BED()' with selected samples for sex and phenotype information
• ‘seqGDS2VCF()' failed if there is no ’genotype/data' in the GDS file

SeqArray 1.32.0

NEW FEATURES

• new option 'ret.idx' in 'seqSetFilter()' for unsorted sample and variant indices
• new option 'ret.idx' in 'seqSetFilterAnnotID()' for unsorted variant index
• rewrite the function ‘seqSetFilterPos()': new options ’ref' and 'alt', 'multi.pos=TRUE' by default
• new option 'packed.idx' in 'seqAddValue()' for packing an indexing variable
• new option 'warn' in 'seqSetFilter()' to enable or disable the warning
• new functions 'seqNewVarData()' and 'seqListVarData()' for variable-length data

UTILITIES

• allow no variant in 'seqApply()' and 'seqBlockApply()'
• the list object returned from 'seqGetData()' always have names if there are more than one input variable names

BUG FIXES

• 'seqGDS2VCF()' should output "." instead of NA in the FILTER column
• ‘seqGetData()' should support factor when ’.padNA=TRUE' or '.tolist=TRUE'
• fix 'seqGDS2VCF()' with factor variables
• ‘seqSummary(gds, "$filter")' should return a data frame with zero row if ’annotation/filter' is not a factor

SeqArray 1.30.0

UTILITIES

• show a warning when an unsorted index is used in 'seqSetFilter()'
• show a message if 'seqVCF_Header()' fails
• a new option 'chr_prefix' in 'seqGDS2VCF()'

BUG FIXES

• ‘seqVCF_Header()' fixes ’contig' in the header of VCF if there are different fields

SeqArray 1.28.1

BUG FIXES

• 'seqRecompress(, verbose=FALSE)' works correctly
• 'seqSetFilter(, action="push+set")' should not reset the filter before setting a new filter

SeqArray 1.28.0

NEW FEATURES

• new functions 'seqUnitSlidingWindows()', 'seqUnitApply()', 'seqUnitFilterCond()'
• new variable "$variant_index", "$sample_index" in 'SeqGetData()', 'seqBlockApply()' and 'seqUnitApply()' to get the indices of selected variants
• new arguments '.padNA' and '.envir' in 'seqGetData()'
• new functions 'seqSetFilterAnnotID()' and 'seqGDS2BED()'
• multicore function in 'seqBED2GDS(, parallel=)'
• new package-wide option 'options(seqarray.nofork=TRUE)' to disable forking
• new option 'minor' in 'seqAlleleFreq()' and 'seqAlleleCount()'
• new option 'verbose' in ‘seqMissing()', 'seqAlleleFreq()' and 'seqAlleleCount()'; ’.progress' is deprecated, but still can be used for compatiblity
• ‘seqAlleleFreq()', 'seqAlleleCount()', 'seqMissing()', 'seqSetFilterCond()' work on ’annotation/format/DS', if 'genotype/data' is not available

UTILITIES

• 'seqAddValue()' adds vectors, matrices and data frame to "annotation/info"
• 'seqBED2GDS()' allows a single file name without the extended file names (.bed, .fam, .bim)
• allele flip in 'seqBED2GDS()' to allow major allele to be reference
• rewrite 'seqGetData()' for faster loading
• significantly improve ‘seqBlockApply()' on ’annotation/info/VARIABLE' (https://github.com/zhengxwen/SeqArray/issues/59)
• add a S3 method 'print.SeqVCFHeaderClass()' for 'seqVCF_Header()'
• new option '.tolist' in 'seqGetData()', 'seqBlockApply()' and 'seqUnitApply()'
• String "." in a VCF file are converted to a blank string (missing value) in 'seqVCF2GDS()'
• add a class name 'SeqVarDataList' to the returned 'list(length, data)' from 'seqGetData()'
• new option 'seqMissing(, per.variant=NA)'
• add 'comment.char=""' to 'seqBED2GDS()'

SeqArray 1.26.2

NEW FEATURES

• multiple variable names are allowed in 'seqGetData(, var.name=)'

BUG FIXES

• fix 'seqGetData(, "genotype", .useraw=NA)' (https://github.com/zhengxwen/SeqArray/issues/58)

SeqArray 1.26.1

BUG FIXES

• fails to correctly select duplicate indices in 'seqSetFilter(f, variant.sel=)'

SeqArray 1.26.0

NEW FEATURES

• new function 'seqAddValue()'

UTILITIES

• RLE chromosome coding in 'seqBED2GDS()'
• change the file name "vignettes/R_Integration.Rmd" to "vignettes/SeqArray.Rmd", so 'vignette("SeqArray")' can work directly
• correct Estimated remaining Time to Complete (ETC) for load balancing in 'seqParallel()'

BUG FIXES

• 'seqBED2GDS(, verbose=FALSE)' should have no display

CHANGES

• use a svg file instead of png in vignettes

SeqArray 1.24.2

NEW FEATURES

• add the compiler information in 'seqSystem()'
• new arguments '.balancing', '.bl_size' and '.bl_progress' in 'seqParallel()' for load balancing

UTILITIES

• improve unix forking processes for load balancing in 'seqParallel()'

BUG FIXES

• fix 'seqSummary()' when no phase data

SeqArray 1.24.0

NEW FEATURES

• a new function 'seqResetVariantID()'
• a new option in 'seqRecompress(, compress="none")' to uncompress all data
• 'seqGetData()' allows a GDS file name in the first argument

SeqArray 1.22.6

BUG FIXES

• '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)
• the bgzf VCF file is truncated in 'seqGDS2VCF()' since the file is not closed appropriately
• invalid chromosomes and position in the output of 'seqMerge()' when merging different samples but same variants

SeqArray 1.22.3

NEW FEATURES

• a new option 'scenario' in 'seqVCF2GDS()' and 'seqBCF2GDS()'

UTILITIES

• more information in 'seqDelete()'

BUG FIXES

• export a haploid VCF file using 'seqGDS2VCF()'
• export VCF without any FORMAT data in 'seqGDS2VCF()'
• export GDS without genotypes in 'seqExport()'
• fix parallel file writing in seqVCF2GDS(), when no genotype

SeqArray 1.22.0

NEW FEATURES

• 'seqSNP2GDS()' imports dosage GDS files
• 'seqVCF_Header()' allows a BCF file as an input
• a new function 'seqRecompress()'
• a new function 'seqCheck()' for checking the data integrity of a SeqArray GDS file
• 'seqGDS2SNP()' exports dosage GDS files

UTILITIES

• avoid duplicated meta-information lines in 'seqVCF2GDS()' and 'seqVCF_Header()'
• require >= R_v3.5.0, since reading from connections in text mode is buffered
• 'seqDigest()' requires the digest package
• optimization in reading genotypes from a subset of samples (according to gdsfmt_1.17.5)

BUG FIXES

• 'seqVCF2GDS()' and 'seqVCF_Header()' are able to import site-only VCF files (i.e., VCF with no sample)
• fix 'seqVCF2GDS()' and 'seqBCF2GDS()' since reading from connections in text mode is buffered in R >= v3.5.0

SeqArray 1.20.1

BUG FIXES

• 'seqExport()' fails to export haploid data (e.g., Y chromosome)
• 'seqVCF2GDS()' fails to convert INFO variables when Number="R"

SeqArray 1.20.0

NEW FEATURES

• 'seqGDS2VCF()' outputs a bgzip vcf file for tabix indexing
• two more options "Ultra" and "UltraMax" in 'seqStorageOption()'
• '@chrom_rle_val' and '@chrom_rle_len' are added to a GDS file for faster chromosome indexing
• new function 'seqBCF2GDS()' (requiring the software bcftools)
• new function 'seqSetFilterPos()'
• new variable "$dosage_alt" in 'seqGetData()' and 'seqApply()'
• import VCF files with no GT in 'seqVCF2GDS()'

UTILITIES

• 'seqDigest(f, "annotation/filter")' works on a factor variable
• improve the computational efficiency of 'seqMerge()' to avoid genotype recompression by padding the 2-bit genotype array in bytes
• significantly improve 'seqBlockApply()' (its speed is close to 'seqApply()')
• reduce the overhead in 'seqSetFilter(, variant.sel=...)'

SeqArray 1.18.2

BUG FIXES

• fix an issue: 'seqSetFilterChrom()' extends a genomic range upstream and downstream 1bp
• use '.onLoad()' instead of '.onAttach()' to fix https://support.bioconductor.org/p/104405/#104443

SeqArray 1.18.0

NEW FEATURES

• progress information: showing overall running time when completed
• new variable names "$ref" and "$alt" can be used in 'seqGetData()' and 'seqBlockApply()'
• new argument '.progress' in 'seqDigest()'
• new argument 'ref.allele' in 'seqAlleleCount()'
• new variable name "$chrom_pos_allele" can be used in 'seqGetData()' and 'seqBlockApply()'

UTILITIES

• move VariantAnnotation to the suggest field from the import field
• remove an unused argument '.list_dup' in 'seqBlockApply()'
• slightly improve the computational efficiency of ‘seqAlleleFreq()' and 'seqAlleleCount()' when ’ref.allele=0'
• ‘seqGetData(f, "$chrom_pos")' outputs characters with the format ’chromosome:position' instead of 'chromosome_position'

BUG FIXES

• fix the unexpected behaviors in 'seqSetFilter(, action="push")' and 'seqSetFilter(, action="push+intersect")'
• 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)
• fix a bug in 'seqSNP2GDS()' for inverted genotypes during importing data from SNP GDS files (https://github.com/zhengxwen/SeqArray/issues/22)
• fix an issue of no phase data in 'seqExport()'

SeqArray 1.16.0

• a new argument 'intersect' in 'seqSetFilter()' and 'seqSetFilterChrom()'
• a new function 'seqSetFilterCond()'
• 'seqVCF2GDS()' allows arbitrary numbers of different alleles if REF and ALT in VCF are missing
• optimize internal indexing for FORMAT annotations to avoid reloading the indexing from the GDS file
• a new CITATION file
• 'LZMA_RA' is the default compression method in 'seqBED2GDS()' and 'seqSNP2GDS()'
• 'seqVCF_Header()' correctly calculates ploidy with missing genotypes

SeqArray 1.14.1

• The default compression setting in 'seqVCF2GDS()' and 'seqMerge()' is changed from "ZIP_RA" to "LZMA_RA"
• '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

SeqArray 1.12.9

• the version number was bumped for the Bioconductor release version 3.3
• 'seqVCF_SampID()', 'seqVCF_Header()' and 'seqVCF2GDS()' allow a connection object instead of a file name
• "$num_allele" is allowed in 'seqGetData()' and 'seqApply()' (the numbers of distinct alleles)
• a new option '.progress' in 'seqAlleleFreq()', 'seqMissing()' and 'seqAlleleCount()'
• 'as.is' can be a 'gdsn.class' object in 'seqApply()'
• v1.12.7: a new argument 'parallel' in 'seqApply()', BiocParallel integration in 'seqParallel()' and a new function 'seqBlockApply()'
• v1.12.8: a new function 'seqGetParallel()'

SeqArray 1.12.0

• 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)
• ~4x speedup in the sequential version of 'seqVCF2GDS()', and 'seqVCF2GDS()' can run in parallel
• variables in "annotation/format/" should be two-dimensional as what mentioned in the vignette.
• rewrite 'seqSummary()'
• a new vignette file with Rmarkdown format (replacing SeqArray-JSM2013.pdf)
• bug fix in 'seqBED2GDS()' if the total number of genotypes > 2^31 (integer overflow)
• bug fixes in 'seqMerge()' if chromosome and positions are not unique
• 'seqStorage.Option()' is renamed to 'seqStorageOption()'
• new function 'seqDigest()'
• 'seqVCF.Header()' is renamed to 'seqVCF_Header()', 'seqVCF.SampID()' is renamed to 'seqVCF_SampID()'
• seqSetFilter(): 'samp.sel' is deprecated since v1.11.12, please use 'sample.sel' instead
• accelerate reading genotypes with SSE2(+13%) and AVX2(+23%)
• new function 'seqSystem()'
• allow "$dosage" in 'seqGetData()' and 'seqApply()' for the dosages of reference allele
• accelerate 'seqSetFilterChrom()' and allow a selection with multiple regions
• new methods '\S4method{seqSetFilter}{SeqVarGDSClass, GRanges}()' and '\S4method{seqSetFilter}{SeqVarGDSClass, GRangesList}()'
• 'as.is' in ‘seqApply()' allows a ’connection' object (created by file, gzfile, etc)
• 'seqSummary(f, "genotype")$seldim' returns a vector with 3 integers (ploidy, # of selected samples, # of selected variants) instead of 2 integers

SeqArray 1.10.6

• fix a memory issue in ‘seqAlleleFreq()' when ’ref.allele' is a vector
• ‘seqSetFilter()' allows numeric vectors in ’samp.sel' and 'variant.sel'
• 'seqSummary()' returns ploidy and reference
• 'seqStorage.Option()' controls the compression level of FORMAT/DATA
• ‘seqVCF2GDS()' allows extract part of VCF files via ’start' and 'count'
• 'seqMerge()' combines multiple GDS files with the same samples
• export methods for compatibility with VariantAnnotation
• a new argument '.useraw' in 'seqGetFilter()'
• a new argument 'allow.duplicate' in 'seqOpen()'
• fix a bug in 'seqParallel()' (https://github.com/zhengxwen/SeqArray/issues/11) and optimize its performance
• 'gdsfile' could be NULL in 'seqParallel()'

SeqArray 1.10.0

• a new function 'seqGDS2SNP()'
• supported by the SNPRelate package
• support 'seqApply(..., margin="by.sample")'
• new functions 'seqOptimize()', 'seqMissing()', 'seqAlleleFreq()', 'seqNumAllele()' and 'seqSetFilterChrom()'
• "intersection" and "push+intersection" in 'seqSetFilter()'
• parallel implementation in 'seqNumAllele()', 'seqMissing()' and 'seqAlleleFreq()'
• a new function 'seqExport()'
• new argument ".useraw" in 'seqApply()'
• fix a bug for duplicated "variant.id", https://github.com/zhengxwen/SeqArray/issues/7
• fix an issue of 'seqVCF2GDS()' when there are duplicated format or info ID
• improve access speed (+50%, benchmark on calling seqApply(..., FUN=function(x) {}))
• new functions 'seqSNP2GDS()', 'seqBED2GDS()', 'seqAlleleCount()' and 'seqResetFilter()'
• 'seqCompress.Option()' is renamed to 'seqStorage.Option()'
• "ZIP_RA" is the default value in 'seqStorageOption()' and other functions instead of "ZIP_RA.max"
• 'seqSetFilter()' becomes a S4 method

SeqArray 1.8.0

• bug fix in getting genotypes if position > 2^31
• add an option 'ignore.chr.prefix' to the function 'seqVCF2GDS()'
• 'seqVCF2GDS()' ignores the INFO or FORMAT variables if they are not defined ahead
• a new action 'push+set' in the function 'seqSetFilter()'
• bug fix if 'requireNamespace("SeqArray")' is called from other packages

SeqArray 1.6.0

• fix a bug in 'seqVCF2GDS()' when the values in the FILTER column are all missing
• enhance 'seqVCF.Header()'
• support the LinkingTo mechanism
• fix the error in haploid genotypes (Y chromosome)

SeqArray 1.4.0

• update according to the new version of VariantAnnotation
• update test codes to avoid the conflict
• bumped version as all packages that depend on Rcpp must be rebuilt
• modify to new biocViews to DESCRIPTION file

SeqArray 1.2.0

• add a new argument "action" to the function 'seqSetFilter()'
• add a new function 'seqInfoNewVar' which allows adding new variables to the INFO fields
• minor bug fix in asVCF
• update man page "SeqVarGDSClass-class.Rd" with new methods
• in DESCRIPTION, BiocGenerics listed in "Suggests" instead of "Imports" as suggested by R CMD check
• bug fix in seqDelete
• revise the function 'seqTranspose' according to the update of gdsfmt (v1.0.0)
• revise the argument 'var.index' in the function 'seqApply()'
• basic supports of 'GRanges' and 'DNAStringSetList'
• added methods 'qual', 'filt', 'asVCF'
• 'granges' method uses length of reference allele to set width
• minor bug fix to avoid 'seqGetData()' crashing when no value returned from a variable-length variable
• update documents

SeqArray 1.0.0

• the version number was bumped for the Bioconductor release version

SeqArray 0.99.0

• initial Bioconductor package submission