# Uses of Class
org.snpeff.fileIterator.FileIterator

Packages that use FileIterator
Package
Description
org.snpeff.fileIterator
org.snpeff.fileIterator.microCosm
org.snpeff.ped

## Uses of FileIterator in org.snpeff.fileIterator

Subclasses of FileIterator in org.snpeff.fileIterator
Modifier and Type
Class
Description
`class`
`BedFileIterator`
Opens a sequence change file and iterates over all intervals in BED format.
`class`
`BigBedFileIterator`
FileIterator for BigBed features WARNING: Removed in 2022-01 due to dependency on IGV's code (which depends on Log4j, which has a major security issue) Note: I use Broad's IGV code to do all the work, this is just a wrapper
`class`
`BlastResultFileIterator`
Iterate on each line of a GWAS catalog (TXT format)
`class`
`FastaFileIterator`
Opens a fasta file and iterates over all fasta sequences in the file
`class`
`GenericMarkerFileIterator`
Opens a file and creates generic markers (one per line)
`class`
`Gff3FileIterator`
Opens a sequence change file and iterates over all intervals in GFF3 format.
`class`
`LineClassFileIterator<T>`
Iterate on each line.
`class`
`LineFileIterator`
Iterate on each line in this file
`class`
`LineSeqFileIterator`
One line per sequence.
`class`
`MarkerFileIterator<M extends Marker>`
Opens a Marker file and iterates over all markers
`class`
`MatrixEntryFileIterator`
Iterate on each line of a file, creating a MatrixEntry
`class`
`MotifFileIterator`
Opens a regulation file and create Motif elements.
`class`
`RegulationBedFileIterator`
Opens a GFF3 file and create regulatory elements.
`class`
`RegulationFileIterator`
Opens a regulation file and create Regulation elements.
`class`
`RegulationGffFileIterator`
Opens a GFF3 file and create regulatory elements.
`class`
`SamFileIterator`
Reads a SAM file Note: This is a very 'rustic' reader (we should use Picard's API instead)
`class`
`VariantFileIterator`
Opens a sequence change file and iterates over all sequence changes
`class`
`VariantTxtFileIterator`
Opens a sequence change file and iterates over all sequence changes TXT Format: Tab-separated format, containing five columns that correspond to: chr \t position \t refSeq \t newSeq \t strand \t quality \t coverage \t id \n Fields strand, quality, coverage and id are optional E.g.
`class`
`VcfFileIterator`
Opens a VCF file and iterates over all entries (i.e.
`class`
`VcfHapMapFileIterator`
Opens a Hapmap phased file and iterates over all entries, returning VcfEntries for each line Note: Each HapMap file has one chromosome.

## Uses of FileIterator in org.snpeff.fileIterator.microCosm

Subclasses of FileIterator in org.snpeff.fileIterator.microCosm
Modifier and Type
Class
Description
`class`
`MicroCosmFileIterator`
Iterate on each line of a MicroCosm predictions References: http://www.ebi.ac.uk/enright-srv/microcosm/

## Uses of FileIterator in org.snpeff.ped

Subclasses of FileIterator in org.snpeff.ped
Modifier and Type
Class
Description
`class`
`PedFileIterator`
PED file iterator (PED file from PLINK) Reference: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml