Class: Status

Inherits:
Object
  • Object
show all
Defined in:
lib/status.rb

Overview

Class containing methods to records demultiplexing status.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(samples) ⇒ Status

Internal: Constructor method to initialize a Status object, which contains the following instance variables initialized to 0:

@count           - Number or reads.
@match           - Number of reads found in index.
@undetermined    - Number of reads not found in index.
@index1_bad_mean - Number of reads dropped due to bad mean in index1.
@index2_bad_mean - Number of reads dropped due to bad mean in index2.
@index1_bad_min  - Number of reads dropped due to bad min in index1.
@index2_bad_min  - Number of reads dropped due to bad min in index2.

samples - Array of Sample objects.

Examples

Status.new(samples)
# => <Status>

Returns a Status object.



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# File 'lib/status.rb', line 47

def initialize(samples)
  @samples         = samples
  @count           = 0
  @match           = 0
  @undetermined    = 0
  @index1_bad_mean = 0
  @index2_bad_mean = 0
  @index1_bad_min  = 0
  @index2_bad_min  = 0
  @time_start      = Time.now
end

Instance Attribute Details

#count ⇒ Object

Returns the value of attribute count.



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# File 'lib/status.rb', line 26

def count
  @count
end

#index1_bad_mean ⇒ Object

Returns the value of attribute index1_bad_mean.



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# File 'lib/status.rb', line 26

def index1_bad_mean
  @index1_bad_mean
end

#index1_bad_min ⇒ Object

Returns the value of attribute index1_bad_min.



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# File 'lib/status.rb', line 26

def index1_bad_min
  @index1_bad_min
end

#index2_bad_mean ⇒ Object

Returns the value of attribute index2_bad_mean.



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# File 'lib/status.rb', line 26

def index2_bad_mean
  @index2_bad_mean
end

#index2_bad_min ⇒ Object

Returns the value of attribute index2_bad_min.



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# File 'lib/status.rb', line 26

def index2_bad_min
  @index2_bad_min
end

#match ⇒ Object

Returns the value of attribute match.



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# File 'lib/status.rb', line 26

def match
  @match
end

#undetermined ⇒ Object

Returns the value of attribute undetermined.



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# File 'lib/status.rb', line 26

def undetermined
  @undetermined
end

Instance Method Details

#save(file) ⇒ Object

Internal: Method to save stats to the log file ‘Demultiplex.log’ in the output directory.

Returns nothing.



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# File 'lib/status.rb', line 83

def save(file)
  File.open(file, 'w') do |ios|
    ios.puts self
  end
end

#to_s ⇒ Object

Internal: Method to format a String from a Status object. This is done by adding the relevant instance variables to a Hash and return this as an YAML String.

Returns a YAML String.



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# File 'lib/status.rb', line 64

def to_s
  { count:                @count,
    match:                @match,
    undetermined:         @undetermined,
    undetermined_percent: undetermined_percent,
    index1_bad_mean:      @index1_bad_mean,
    index2_bad_mean:      @index2_bad_mean,
    index1_bad_min:       @index1_bad_min,
    index2_bad_min:       @index2_bad_min,
    sample_ids:           @samples.map(&:id),
    index1:               uniq_index1,
    index2:               uniq_index2,
    time_elapsed:         time_elapsed }.to_yaml
end