BedFileIterator |
Opens a sequence change file and iterates over all intervals in BED format.
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BigBedFileIterator |
FileIterator for BigBed features
Note: I use Broad's IGV code to do all the work, this is just a wrapper
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BinSeqFileIterator<T extends BinarySequence> |
Reads all sequences from a file
Warning: You should always call "close()" at the end of the iteration.
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BlastResultEntry |
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BlastResultFileIterator |
Iterate on each line of a GWAS catalog (TXT format)
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DnaSeqFileIterator |
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DnaSeqIdFileIterator |
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DnaSeqPeFileIterator |
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FastaFileIterator |
Opens a fasta file and iterates over all fasta sequences in the file
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FastqFileIterator |
Opens 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.
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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
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GenericMarkerFileIterator |
Opens a file and creates generic markers (one per line)
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Gff3FileIterator |
Opens a sequence change file and iterates over all intervals in GFF3 format.
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GuessTableTypes |
Given a table in a TXT file, try to guess the value types for each column
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LineClassFileIterator<T> |
Iterate on each line.
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LineFileIterator |
Iterate on each line in this file
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LineSeqFileIterator |
One line per sequence.
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MarkerFileIterator<M extends Marker> |
Opens a Marker file and iterates over all markers
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MatrixEntry |
A simple entry in a 'Matrix' file
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MatrixEntryFileIterator |
Iterate on each line of a file, creating a MatrixEntry
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MotifFileIterator |
Opens a regulation file and create Motif elements.
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NullReader |
A buffered reader for a file.
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RegulationBedFileIterator |
Opens a GFF3 file and create regulatory elements.
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RegulationFileIterator |
Opens a regulation file and create Regulation elements.
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RegulationGffFileIterator |
Opens a GFF3 file and create regulatory elements.
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SamFileIterator |
Reads a SAM file
Note: This is a very 'rustic' reader (we should use Picard's API instead)
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SeekableBufferedReader |
A buffered reader for a file.
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TableFile |
Load a table from a file.
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VariantFileIterator |
Opens a sequence change file and iterates over all sequence changes
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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.
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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.
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VcfHapMapFileIterator |
Opens a Hapmap phased file and iterates over all entries, returning VcfEntries for each line
Note: Each HapMap file has one chromosome.
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