Uses of Package
org.snpeff.fileIterator
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Classes in org.snpeff.fileIterator used by org.snpeff Class Description RegulationFileIterator Opens a regulation file and create Regulation elements. -
Classes in org.snpeff.fileIterator used by org.snpeff.fileIterator Class Description BinSeqFileIterator Reads all sequences from a file Warning: You should always call "close()" at the end of the iteration.BlastResultEntry FileIterator Opens a file and iterates over all objectsin the file Note: The file is not loaded in memory, thus allows to iterate over very large files LineClassFileIterator Iterate on each line.LineFileIterator Iterate on each line in this fileMarkerFileIterator Opens a Marker file and iterates over all markersRegulationFileIterator Opens a regulation file and create Regulation elements.VariantFileIterator Opens a sequence change file and iterates over all sequence changes -
Classes in org.snpeff.fileIterator used by org.snpeff.fileIterator.microCosm Class Description FileIterator Opens a file and iterates over all objectsin the file Note: The file is not loaded in memory, thus allows to iterate over very large files LineClassFileIterator Iterate on each line. -
Classes in org.snpeff.fileIterator used by org.snpeff.genBank Class Description LineFileIterator Iterate on each line in this file -
Classes in org.snpeff.fileIterator used by org.snpeff.ped Class Description FileIterator Opens a file and iterates over all objectsin the file Note: The file is not loaded in memory, thus allows to iterate over very large files -
Classes in org.snpeff.fileIterator used by org.snpeff.snpEffect Class Description VcfFileIterator Opens a VCF file and iterates over all entries Format: VCF 4.1 Reference: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 Old 4.0 format: http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0 1. -
Classes in org.snpeff.fileIterator used by org.snpeff.snpEffect.commandLine Class Description VcfFileIterator Opens a VCF file and iterates over all entries Format: VCF 4.1 Reference: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 Old 4.0 format: http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0 1. -
Classes in org.snpeff.fileIterator used by org.snpeff.vcf Class Description VcfFileIterator Opens a VCF file and iterates over all entries Format: VCF 4.1 Reference: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 Old 4.0 format: http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0 1.