A B C D E F G I K L M N O P Q R S T V W

G

Gene - Class in edu.unc.csbio.data
The class Gene inherits abstract class Feature and contains information of gene.
Gene(String, String, String, Transcript) - Constructor for class edu.unc.csbio.data.Gene
A constructor for Gene object
genePool - Static variable in class edu.unc.csbio.RNASim.MainCmdline
a TreeMap that maps a string to a gene
generate(Read[]) - Method in class edu.unc.csbio.RNASim.PerfectQualityGenerator
given a read, this method generates perfect quality score for every position of the read
generate(Read[]) - Method in class edu.unc.csbio.RNASim.QualityGenerator
An abstract method of generate(Read[] r)
generate(String) - Method in class edu.unc.csbio.RNASim.ReadGenerator
Randomly sample a fragment from a transcript sequence, and then return its both ends.
generate(Read[]) - Method in class edu.unc.csbio.RNASim.RealQualityGenerator
Generate read quality score by sampling real Fastq file.
GenerateSequence() - Static method in class edu.unc.csbio.RNASim.MainCmdline
this method generate read sequence from given Config file
GenerateSequenceForGenes(String) - Static method in class edu.unc.csbio.RNASim.MainCmdline
Given a chromosome, this method call public static void GenerateSequenceForSingleGene(Gene g, SequenceBuffer buffer) throws IOException on all genes of that chromosome, and prints out total genes, reads and transcripts associated with chromosome.
GenerateSequenceForSingleGene(Gene, SequenceBuffer) - Static method in class edu.unc.csbio.RNASim.MainCmdline
given a gene, this method generates read and appends read information to output fq file
genes - Static variable in class edu.unc.csbio.RNASim.MainCmdline
an array that stores the genes
get(int, int) - Method in class edu.unc.csbio.data.ExtendedSequenceBuffer
Get the sequence for the region [start, end] including structure variants
get(int, int) - Method in class edu.unc.csbio.data.SequenceBuffer
Get the sequence for the region [start, end]
get(String) - Static method in class edu.unc.csbio.RNASim.Config
the method will get the configuration file/data by key
getChromosome() - Method in class edu.unc.csbio.data.Feature
Get the chromosome
getConfigFromArgs(String[]) - Method in class edu.unc.csbio.RNASim.Config
read command line and get the configuration data.
getData(String, int, int) - Static method in class edu.unc.csbio.util.BigFaReader
this method is for getting data given start and end position in one chromosome
getData(String, int, int) - Static method in class edu.unc.csbio.util.FaReader
this method is for getting data within start and end position
getEnd() - Method in class edu.unc.csbio.data.Feature
Get the offset of the end position from the beginning of the chromosome.
getId() - Method in class edu.unc.csbio.data.Transcript
the method to get id of transcript
getInserted() - Method in class edu.unc.csbio.data.Insertion
 
getLength() - Method in class edu.unc.csbio.data.Exon
A method to get exon length
getLength() - Method in class edu.unc.csbio.data.Feature
Get the number of base pairs in the sequence related to this feature.
getLength() - Method in class edu.unc.csbio.data.Gene
The method to get the exon part length of the gene
getLength() - Method in class edu.unc.csbio.data.Insertion
Get the length of the insertion, which is the length of the inserted sequence.
getLength() - Method in class edu.unc.csbio.data.Transcript
The method to get the exon part length of the transcript
getRange() - Method in class edu.unc.csbio.data.Feature
Get the size of the spanning/effective range of this feature, from start position to end position in the reference coordinate.
getSequence(SequenceBuffer) - Method in class edu.unc.csbio.data.Exon
A method to get the sequence of an exon from a mother sequence (a sequence buffer).
getSequence(SequenceBuffer) - Method in class edu.unc.csbio.data.Transcript
The method to get a transcript sequence from a sequence buffer.
getStart() - Method in class edu.unc.csbio.data.Feature
Get the offset of the start position from the beginning of the chromosome.
getTranscripts() - Method in class edu.unc.csbio.data.Gene
The method to get transcripts in the gene
GTFParser - Class in edu.unc.csbio.util
A GTF Parser conforms to GTF2.2 (http://mblab.wustl.edu/GTF22.html)
GTFParser() - Constructor for class edu.unc.csbio.util.GTFParser
 

A B C D E F G I K L M N O P Q R S T V W