Package org.snpeff.fileIterator
package org.snpeff.fileIterator
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ClassesClassDescriptionOpens a sequence change file and iterates over all intervals in BED format.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 wrapperBinSeqFileIterator<T extends BinarySequence>Reads all sequences from a file Warning: You should always call "close()" at the end of the iteration.Iterate on each line of a GWAS catalog (TXT format)Opens a fasta file and iterates over all fasta sequences in the fileOpens 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
in the file Note: The file is not loaded in memory, thus allows to iterate over very large files Opens a file and creates generic markers (one per line)Opens a sequence change file and iterates over all intervals in GFF3 format.Given a table in a TXT file, try to guess the value types for each columnIterate on each line.Iterate on each line in this fileOne line per sequence.MarkerFileIterator<M extends Marker>Opens a Marker file and iterates over all markersA simple entry in a 'Matrix' fileIterate on each line of a file, creating a MatrixEntryOpens a regulation file and create Motif elements.A buffered reader for a file.Opens a GFF3 file and create regulatory elements.Opens a regulation file and create Regulation elements.Opens a GFF3 file and create regulatory elements.Reads a SAM file Note: This is a very 'rustic' reader (we should use Picard's API instead)A buffered reader for a file.Load a table from a file.Opens a sequence change file and iterates over all sequence changesOpens 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.Opens a VCF file and iterates over all entries (i.e.Opens a Hapmap phased file and iterates over all entries, returning VcfEntries for each line Note: Each HapMap file has one chromosome.