Uses of Class
org.snpeff.fileIterator.FileIterator
Packages that use FileIterator
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Uses of FileIterator in org.snpeff.fileIterator
Subclasses of FileIterator in org.snpeff.fileIteratorModifier and TypeClassDescriptionclassOpens a sequence change file and iterates over all intervals in BED format.classFileIterator 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 wrapperclassIterate on each line of a GWAS catalog (TXT format)classOpens a fasta file and iterates over all fasta sequences in the fileclassOpens a file and creates generic markers (one per line)classOpens a sequence change file and iterates over all intervals in GFF3 format.classIterate on each line.classIterate on each line in this fileclassOne line per sequence.classMarkerFileIterator<M extends Marker>Opens a Marker file and iterates over all markersclassIterate on each line of a file, creating a MatrixEntryclassOpens a regulation file and create Motif elements.classOpens a GFF3 file and create regulatory elements.classOpens a regulation file and create Regulation elements.classOpens a GFF3 file and create regulatory elements.classReads a SAM file Note: This is a very 'rustic' reader (we should use Picard's API instead)classOpens a sequence change file and iterates over all sequence changesclassOpens 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.classOpens 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.classOpens 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.microCosmModifier and TypeClassDescriptionclassIterate 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.pedModifier and TypeClassDescriptionclassPED file iterator (PED file from PLINK) Reference: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml