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 TypeClassDescriptionclass
Opens a sequence change file and iterates over all intervals in BED format.class
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 wrapperclass
Iterate on each line of a GWAS catalog (TXT format)class
Opens a fasta file and iterates over all fasta sequences in the fileclass
Opens a file and creates generic markers (one per line)class
Opens a sequence change file and iterates over all intervals in GFF3 format.class
Iterate on each line.class
Iterate on each line in this fileclass
One line per sequence.class
MarkerFileIterator<M extends Marker>
Opens a Marker file and iterates over all markersclass
Iterate on each line of a file, creating a MatrixEntryclass
Opens a regulation file and create Motif elements.class
Opens a GFF3 file and create regulatory elements.class
Opens a regulation file and create Regulation elements.class
Opens a GFF3 file and create regulatory elements.class
Reads a SAM file Note: This is a very 'rustic' reader (we should use Picard's API instead)class
Opens a sequence change file and iterates over all sequence changesclass
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
Opens a VCF file and iterates over all entries (i.e.class
Opens 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 TypeClassDescriptionclass
Iterate 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 TypeClassDescriptionclass
PED file iterator (PED file from PLINK) Reference: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml