R/read_simple.R

In WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

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###		Reading
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#
#	returns a data-frame where the rownames are the field names of the VCF
#
vcf_readLineDF <- function( vcffh )	return(	data.frame( .Call("VCF_readLineTSV",vcffh,PACKAGE="WhopGenome"), row.names=.Call("VCF_getFieldNames",vcffh,PACKAGE="WhopGenome") )	)
vcf_readLineDFFiltered <- function( vcffh )	return(	data.frame( .Call("VCF_readLineTSVFiltered",vcffh,PACKAGE="WhopGenome"), row.names=.Call("VCF_getFieldNames",vcffh,PACKAGE="WhopGenome") )	)


#
#	reads a line and returns a vector with the fields of that line
#
vcf_readLineVec <- function( vcffh )	return( .Call("VCF_readLineTSV",vcffh,PACKAGE="WhopGenome")	)
vcf_readLineVecFiltered <- function( vcffh )	.Call("VCF_readLineTSVFiltered",vcffh,PACKAGE="WhopGenome")


#
#	reads a line and stores in 'str'
#
#@ubw : readLineRaw[Filtered] take two arguments (by initial design) but warn when using a (string) variable as second argument
	#	unfiltered
	#
vcf_readLineRaw <- function( vcffh )	.Call("VCF_readLineRaw",vcffh, NA, PACKAGE="WhopGenome")

	#	filtered
	#
vcf_readLineRawFiltered <- function( vcffh )	.Call("VCF_readLineRawFiltered",vcffh, NA, PACKAGE="WhopGenome")

#
#
#
vcf_countBiallelicSNPs <- function( vcffh )	.Call("VCF_countBiallelicSNPs",vcffh,PACKAGE="WhopGenome")
vcf_countSNPs <- function( vcffh )	.Call("VCF_countSNPs",vcffh,PACKAGE="WhopGenome")
vcf_parseNextSNP <- function( vcffh )	.Call("VCF_parseNextSNP",vcffh,PACKAGE="WhopGenome")
vcf_parseNextLine <- function( vcffh )	.Call("VCF_parseNextLine",vcffh,PACKAGE="WhopGenome")
vcf_getChrom <- function( vcffh )	.Call("VCF_getChrom",vcffh,PACKAGE="WhopGenome")
vcf_getPos <- function( vcffh )	.Call("VCF_getPos",vcffh,PACKAGE="WhopGenome")
vcf_getID <- function( vcffh )	.Call("VCF_getID",vcffh,PACKAGE="WhopGenome")
vcf_getRef <- function( vcffh )	.Call("VCF_getRef",vcffh,PACKAGE="WhopGenome")
vcf_getAlt <- function( vcffh )	.Call("VCF_getAlt",vcffh,PACKAGE="WhopGenome")
vcf_getQual <- function( vcffh )	.Call("VCF_getQual",vcffh,PACKAGE="WhopGenome")
vcf_getFilter <- function( vcffh )	.Call("VCF_getFilter",vcffh,PACKAGE="WhopGenome")
vcf_getInfo <- function( vcffh )	.Call("VCF_getInfo",vcffh,PACKAGE="WhopGenome")
vcf_getInfoField <- function( vcffh, fieldnam )	.Call("VCF_getInfoField",vcffh,fieldnam,PACKAGE="WhopGenome")
vcf_getFormat <- function( vcffh )	.Call("VCF_getFormat",vcffh,PACKAGE="WhopGenome")
vcf_getSample <- function( vcffh, stridx )	.Call("VCF_getSample",vcffh,stridx,PACKAGE="WhopGenome")

#
#
#
VCF_read_snp_diplo_bial_int_altpresence <- function( vcffh, mat ) .Call("read_snp_diplo_bial_int_altpresence", vcffh, mat, PACKAGE="WhopGenome" )
VCF_read_snp_diplo_bial_str_allelechars <- function( vcffh, mat ) .Call("read_snp_diplo_bial_str_allelechars", vcffh, mat, PACKAGE="WhopGenome" )
VCF_read_snp_diplo_bial_str_01 <- function( vcffh, mat ) .Call("read_snp_diplo_bial_str_01", vcffh, mat, PACKAGE="WhopGenome" )
VCF_read_snp_diplo_bial_int_nuclcodes <- function( vcffh, mat ) .Call("read_snp_diplo_bial_int_nuclcodes", vcffh, mat, PACKAGE="WhopGenome" )
VCF_read_snp_diplo_bial_str_nuclcodes <- function( vcffh, mat ) .Call("read_snp_diplo_bial_str_nuclcodes", vcffh, mat, PACKAGE="WhopGenome" )



#
#	R function does the same as the C function:
#		call VCF_snpmat_diplo_bial_hasalt_filtered instead
#
VCF_read_snp_diplo_bial_int_altpresence <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_hasalt_filtered", vcffh, mat, PACKAGE="WhopGenome" )


#
#	new, improved SNP-matrix read functions
#
VCF_snpmat_diplo_bial_geno_filtered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_geno_filtered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_anyal_geno_filtered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_anyal_geno_filtered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_bial_geno_unfiltered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_geno_unfiltered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_anyal_geno_unfiltered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_anyal_geno_unfiltered", vcffh, mat, PACKAGE="WhopGenome" )

VCF_snpmat_diplo_bial_ishet_filtered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_ishet_filtered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_anyal_ishet_filtered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_anyal_ishet_filtered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_bial_ishet_unfiltered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_ishet_unfiltered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_anyal_ishet_unfiltered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_anyal_ishet_unfiltered", vcffh, mat, PACKAGE="WhopGenome" )

VCF_snpmat_diplo_bial_hasalt_filtered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_hasalt_filtered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_bial_hasalt_unfiltered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_hasalt_unfiltered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_anyal_hasalt_filtered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_anyal_hasalt_filtered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_anyal_hasalt_unfiltered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_anyal_hasalt_unfiltered", vcffh, mat, PACKAGE="WhopGenome" )

VCF_snpmat_diplo_bial_nucodes_filtered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_nucodes_filtered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_bial_nucodes_unfiltered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_nucodes_unfiltered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_anyal_nucodes_filtered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_anyal_nucodes_filtered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_diplo_anyal_nucodes_unfiltered <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_anyal_nucodes_unfiltered", vcffh, mat, PACKAGE="WhopGenome" )

VCF_snpmat_anyplo_bial_nucodes_filtered <- function( vcffh, mat ) .Call("VCF_snpmat_anyplo_bial_nucodes_filtered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_anyplo_bial_nucodes_unfiltered <- function( vcffh, mat ) .Call("VCF_snpmat_anyplo_bial_nucodes_unfiltered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_anyplo_anyal_nucodes_filtered <- function( vcffh, mat ) .Call("VCF_snpmat_anyplo_anyal_nucodes_filtered", vcffh, mat, PACKAGE="WhopGenome" )
VCF_snpmat_anyplo_anyal_nucodes_unfiltered <- function( vcffh, mat ) .Call("VCF_snpmat_anyplo_anyal_nucodes_unfiltered", vcffh, mat, PACKAGE="WhopGenome" )

##	Obsolete functions / function names and their redirections
##
VCF_readIntoCodeMatrix <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_nucodes_filtered", vcffh, mat, PACKAGE="WhopGenome" )
read_snp_diplo_bial_int_altpresence <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_hasalt_filtered", vcffh, mat, PACKAGE="WhopGenome" )
read_snp_diplo_bial_int_nuclcodes <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_nucodes_filtered", vcffh, mat, PACKAGE="WhopGenome" )
read_snp_diplo_bial_str_allelechars <- function( vcffh, mat ) .Call("VCF_snpmat_diplo_bial_geno_filtered", vcffh, mat, PACKAGE="WhopGenome" )
read_snp_diplo_bial_str_01 <- function( vcffh, mat )	stop("Not supported anymore: read_snp_diplo_bial_str_01 - use VCF_snpmat_diplo_bial_hasalt_(un)filtered instead")
read_snp_diplo_bial_str_nuclcodes <- function( vcffh, mat )	stop("Not supported anymore: read_snp_diplo_bial_str_nuclcodes - use VCF_snpmat_diplo_bial_nucodes_(un)filtered instead")