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java.lang.Objectedu.unc.csbio.RNASim.MainCmdline
public class MainCmdline
The class MainCmdline
is the main class
Field Summary | |
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(package private) static java.util.HashMap<java.lang.String,java.lang.Double> |
abundancePool
a Hashmap that maps a string to an abundance value |
(package private) static int |
annotLimit
max number of lines allowed for annotation file |
(package private) static java.lang.String |
chrom
this will be the prefix of the all read ID |
(package private) static java.lang.String |
chromMatching
specify the matching of chromosome string, Exact or Fuzzy. |
(package private) static java.util.TreeSet<java.lang.String> |
chromPool
a TreeSet that stores the chromosome names |
(package private) static double |
coverageFactor
coverage factor = total read length / total sequence size |
(package private) static double |
distMean
distribution mean value, will be used when calculating abundance. |
(package private) static double |
expressionPercentage
percentage of gene that will be expressed |
(package private) static int |
fragMaxLength
maximum sequence length |
(package private) static int |
fragMinLength
minimum sequence length |
(package private) static java.util.TreeMap<java.lang.String,Gene> |
genePool
a TreeMap that maps a string to a gene |
(package private) static Gene[] |
genes
an array that stores the genes |
(package private) static java.lang.String |
IDPREFIX
this will be the prefix of the all read ID |
(package private) static int |
inputBufferSize
input buffer size |
(package private) static FqWriter |
out1
the file location of fq writer file (for first pair end read) |
(package private) static FqWriter |
out2
the file location of fq writer file (for second pair end read) |
(package private) static int |
outputBufferSize
output buffer size |
(package private) static int |
processBufferSize
buffer size for accumulating gene range |
(package private) static QualityGenerator |
qg
a qualityGenerator |
(package private) static int |
readLength
read length |
(package private) static long |
startTime
time when program start running |
(package private) static java.util.HashMap<java.lang.String,java.util.ArrayList<Feature>> |
svPool
an array that stores the structure variants |
(package private) static double |
tDistDOF
the value used to calculate distMean. |
(package private) static long |
totalGenes
total number of the genes |
(package private) static long |
totalGenesByChrom
total number of genes in a chromosome |
(package private) static long |
totalReads
total number of the reads |
(package private) static long |
totalReadsByChrom
total number of reads in a chromosome |
(package private) static long |
totalTranscripts
total number of transcripts |
(package private) static long |
totalTranscriptsByChrom
total number of transcripts in a chromosome |
(package private) static java.util.TreeMap<java.lang.String,Transcript> |
transcriptPool
a TreeMap that maps a string to a transcript |
Constructor Summary | |
---|---|
MainCmdline()
|
Method Summary | |
---|---|
static void |
abort(java.lang.Exception e)
the method to abort the program |
static void |
BuildAbundance(java.lang.String abundanceFn)
this method creates abundance file with default settings |
static void |
GenerateSequence()
this method generate read sequence from given Config file |
static void |
GenerateSequenceForGenes(java.lang.String chrom)
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. |
static void |
GenerateSequenceForSingleGene(Gene g,
SequenceBuffer buffer)
given a gene, this method generates read and appends read information to output fq file |
static void |
main(java.lang.String[] args)
this is the driver for the whole program |
static void |
printRuntime()
the method to print out the run time of the program |
static void |
ReadAnnotation()
this method reads annotation file. |
static void |
ReadConfig(java.lang.String[] args)
this method read configuration file |
static void |
ReadStructureVariant()
this method read structure variants. |
static void |
ReadTranscriptAbundance()
this method read the transcript abundance from Abundance_File in Config file |
static void |
shuffle(java.lang.Object[] array)
given an array, this method sequentially changes a position with another randomly selected position, for n times, where n is the size of array. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
static java.lang.String IDPREFIX
static java.lang.String chrom
static java.lang.String chromMatching
static int annotLimit
static int inputBufferSize
static int outputBufferSize
static int processBufferSize
static int readLength
static int fragMinLength
static int fragMaxLength
static double coverageFactor
static double expressionPercentage
static double distMean
static double tDistDOF
static long startTime
static java.util.TreeMap<java.lang.String,Transcript> transcriptPool
static java.util.TreeMap<java.lang.String,Gene> genePool
static java.util.HashMap<java.lang.String,java.lang.Double> abundancePool
static java.util.TreeSet<java.lang.String> chromPool
static java.util.HashMap<java.lang.String,java.util.ArrayList<Feature>> svPool
static Gene[] genes
static FqWriter out1
static FqWriter out2
static QualityGenerator qg
static long totalReads
static long totalGenes
static long totalTranscripts
static long totalReadsByChrom
static long totalTranscriptsByChrom
static long totalGenesByChrom
Constructor Detail |
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public MainCmdline()
Method Detail |
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public static void printRuntime()
public static void abort(java.lang.Exception e)
public static void shuffle(java.lang.Object[] array)
public static void ReadConfig(java.lang.String[] args)
args
- the argument array from command linepublic static void ReadAnnotation()
public static void BuildAbundance(java.lang.String abundanceFn)
abundanceFn
- file location of abundance file to be createdpublic static void ReadTranscriptAbundance()
Abundance_File
in Config
file
public static void ReadStructureVariant()
public static void GenerateSequenceForSingleGene(Gene g, SequenceBuffer buffer) throws java.io.IOException
g
- A Gene
objectbuffer
- A SequenceBuffer
object
java.io.IOException
- if an input or output exception occurredpublic static void GenerateSequenceForGenes(java.lang.String chrom) throws java.io.IOException
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.
chrom
- A chromosome
java.io.IOException
- if an input or output exception occurredpublic static void GenerateSequence()
Config
file
public static void main(java.lang.String[] args)
args
- program arguments
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