Uses of Class
org.snpeff.fileIterator.MarkerFileIterator

Packages that use MarkerFileIterator
Package
Description
org.snpeff.fileIterator
 

  • Uses of MarkerFileIterator in org.snpeff.fileIterator

    Subclasses of MarkerFileIterator 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 
    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 
    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 
    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.