new
+Constructor given a vcf file
+
+
+new
+Constructor given a vcf file and the region
+
+
+new
+Constructor given a vcf file, the region and the samples
Parameter: vcffile - The path of a vcf file
+Parameter: region - The region to be constrained
+Parameter: samples - The samples to be constrained. Comma separated list of samples to include (or exclude with "^" prefix).
+
+
+
+variant
+Try to get next variant record. return FALSE if there are no more variants or hit the end of file, otherwise TRUE.
+
+
+chr
+Return the CHROM field of current variant
+
+
+pos
+Return the POS field of current variant
+
+
+id
+Return the CHROM field of current variant
+
+
+ref
+Return the REF field of current variant
+
+
+alt
+Return the ALT field of current variant
+
+
+qual
+Return the QUAL field of current variant
+
+
+filter
+Return the FILTER field of current variant
+
+
+info
+Return the INFO field of current variant
+
+
+infoInt
+Return the tag value of integer type in INFO field of current variant
+
+
+infoFloat
+Return the tag value of float type in INFO field of current variant
+
+
+infoStr
+Return the tag value of string type in INFO field of current variant
+
+
+infoIntVec
+Return the tag value in a vector of integer type in INFO field of current variant
+
+
+infoFloatVec
+Return the tag value in a vector of float type in INFO field of current variant
+
+
+genotypes
+Return the genotype values in a vector of integers
+
+
+formatInt
+Return the tag value of integer type for each sample in FORAMT field of current variant
+
+
+formatFloat
+Return the tag value of float type for each sample in FORAMT field of current variant
+
+
+formatStr
+Return the tag value of string type for each sample in FORAMT field of current variant
+
+
+isSNP
+Test if current variant is exculsively a SNP or not
+
+
+isIndel
+Test if current variant is exculsively a INDEL or not
+
+
+isSV
+Test if current variant is exculsively a SV or not
+
+
+isMultiAllelics
+Test if current variant is exculsively a Multi Allelics or not
+
+
+isMultiAllelicSNP
+Test if current variant is exculsively a Multi Biallelics (SNPs) or not
+
+
+hasSNP
+Test if current variant has a SNP or not
+
+
+hasINDEL
+Test if current variant has a INDEL or not
+
+
+hasINS
+Test if current variant has a INS or not
+
+
+hasDEL
+Test if current variant has a DEL or not
+
+
+hasMNP
+Test if current variant has a MNP or not
+
+
+hasBND
+Test if current variant has a BND or not
+
+
+hasOTHER
+Test if current variant has a OTHER or not
+
+
+hasOVERLAP
+Test if current variant has a OVERLAP or not
+
+
+nsamples
+Return the number of samples
+
+
+samples
+Return a vector of samples id
+
+
+header
+Return the raw string of the vcf header
+
+
+string
+Return the raw string of current variant including newline
+
+
+line
+Return the raw string of current variant without newline
+
+
+output
+Init an output object for streaming out the variants to another vcf
+
+
+write
+Streaming out current variant the output vcf
+
+
+close
+Close the connection to the output vcf
+
+
+setCHR
+Modify the CHR of current variant
+
+
+setID
+Modify the ID of current variant
+
+
+setPOS
+Modify the POS of current variant
+
+
+setRefAlt
+Modify the REF and ALT of current variant
+
+
+setInfoInt
+Modify the given tag of INT type in the INFO of current variant
+
+
+setInfoFloat
+Modify the given tag of FLOAT type in the INFO of current variant
+
+
+setInfoStr
+Modify the given tag of STRING type in the INFO of current variant
+
+
+setPhasing
+Modify the phasing status of each sample
+
+
+setGenotypes
+Modify the genotypes of current variant
+
+
+setFormatInt
+Modify the given tag of INT type in the FORMAT of current variant
+
+
+setFormatFloat
+Modify the given tag of FLOAT type in the FORMAT of current variant
+
+
+setFormatStr
+Modify the given tag of STRING type in the FORMAT of current variant
+
+
+rmInfoTag
+Remove the given tag from the INFO of current variant
+
+
+rmFormatTag
+Remove the given tag from the FORMAT of current variant
+
+
+setVariant
+Modify current variant by adding a vcf line
+
+
+addINFO
+Add a INFO in the header of the vcf
Parameter: id - A string for the tag name
+Parameter: number - A string for the number
+Parameter: type - A string for the type
+Parameter: desc - A string for description of what it means
+
+
+
+addFORMAT
+Add a FORMAT in the header of the vcf
Parameter: id - A string for the tag name
+Parameter: number - A string for the number
+Parameter: type - A string for the type
+Parameter: desc - A string for description of what it means
+
+
+
+