# Package org.snpeff.fileIterator

package org.snpeff.fileIterator

Related Packages
Package
Description
org.snpeff
org.snpeff.fileIterator.microCosm
org.snpeff.fileIterator.parser
Classes
Class
Description
BedFileIterator
Opens a sequence change file and iterates over all intervals in BED format.
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
BinSeqFileIterator<T extends BinarySequence>
Reads all sequences from a file Warning: You should always call "close()" at the end of the iteration.
BlastResultEntry
BlastResultFileIterator
Iterate on each line of a GWAS catalog (TXT format)
DnaSeqFileIterator
DnaSeqIdFileIterator
DnaSeqPeFileIterator
FastaFileIterator
Opens a fasta file and iterates over all fasta sequences in the file
FastqFileIterator
Opens a fastq file and iterates over all fastq sequences in the file Unlike BioJava's version, this one does NOT load all sequences in memory.
FileIterator<T>
Opens a file and iterates over all objects <T> in the file Note: The file is not loaded in memory, thus allows to iterate over very large files
GenericMarkerFileIterator
Opens a file and creates generic markers (one per line)
Gff3FileIterator
Opens a sequence change file and iterates over all intervals in GFF3 format.
GuessTableTypes
Given a table in a TXT file, try to guess the value types for each column
LineClassFileIterator<T>
Iterate on each line.
LineFileIterator
Iterate on each line in this file
LineSeqFileIterator
One line per sequence.
MarkerFileIterator<M extends Marker>
Opens a Marker file and iterates over all markers
MatrixEntry
A simple entry in a 'Matrix' file
MatrixEntryFileIterator
Iterate on each line of a file, creating a MatrixEntry
MotifFileIterator
Opens a regulation file and create Motif elements.
NullReader
A buffered reader for a file.
RegulationBedFileIterator
Opens a GFF3 file and create regulatory elements.
RegulationFileIterator
Opens a regulation file and create Regulation elements.
RegulationGffFileIterator
Opens a GFF3 file and create regulatory elements.
SamFileIterator
Reads a SAM file Note: This is a very 'rustic' reader (we should use Picard's API instead)
SeekableBufferedReader
A buffered reader for a file.
TableFile
Load a table from a file.
VariantFileIterator
Opens a sequence change file and iterates over all sequence changes
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.
VcfFileIterator
Opens a VCF file and iterates over all entries (i.e.
VcfHapMapFileIterator
Opens a Hapmap phased file and iterates over all entries, returning VcfEntries for each line Note: Each HapMap file has one chromosome.