Top Level Namespace

Included Modules

Extended Modules

Defined in:

Method Summary

Instance methods inherited from module CurationTool

build_release(y) : Nil build_release, copy_qc(y) : Nil copy_qc, setup_local(y) : Nil setup_local, setup_tol(y) : Nil setup_tol

Method Detail

def av(l : Array(Float64)) : Float64 #

Returns the arithmetic mean of a Float64 array.


[View source]
def av(l : Array(Int32)) : Float64 #

Returns the arithmetic mean of an Int32 array as Float64.


[View source]
def get_ave(h, l : Array(String)) : Float64 #

Returns the mean value from hash h for the keys in l.


[View source]
def length_and_gc(f) : Tuple(Hash(String, Int32), Hash(String, Float64), Hash(String, Float64), Hash(String, Float64)) #

Computes per-sequence statistics from a gzipped FASTA file. Returns a tuple of hashes keyed by sequence name:

  • sequence length
  • GC content (fraction of G/C bases)
  • repeat fraction (fraction of lowercase/soft-masked bases)
  • stop codon density (occurrences of stop codons per base)

[View source]
def parse_bed_file(f) : Array(String) #

Parses a .contamination.bed file and returns the sequence IDs marked as REMOVE.


[View source]
def parse_decon_file(f) : Array(String) #

Parses a .contamination file and returns the sequence IDs marked as REMOVE.


[View source]