class Depth::FileIO::OutputManager

• Depth::FileIO::OutputManager
• Reference
• Object

Defined in:

depth/io/output_manager.cr

Constant Summary

DIGIT_PAIRS = begin bytes = Bytes.new(200) 100.times do |i| bytes[i &* 2] = 48_u8 &+ (i // 10).to_u8 bytes[(i &* 2) &+ 1] = 48_u8 &+ (i % 10).to_u8 end bytes end

Lookup table of decimal digit pairs "00".."99" for two-digits-at-a-time itoa, halving the divisions vs the per-digit signed Int#to_s.

Constructors

• .new(config : Config)

Instance Method Summary

• #close_all
• #f_global : File | Nil
• #f_perbase : File | HTS::Bgzf | Nil
• #f_quantized : File | HTS::Bgzf | Nil
• #f_region : File | Nil
• #f_regions : File | HTS::Bgzf | Nil
• #f_summary : File | Nil
• #f_thresholds : File | HTS::Bgzf | Nil
• #write_per_base_interval(chrom : String, start : Int32, stop : Int32, depth : Int32)
• #write_quantized_interval(chrom : String, start : Int32, stop : Int32, label : String)
• #write_region_mean(chrom : String, start : Int32, stop : Int32, name : String | Nil, sum : UInt64, length : Int32)
• #write_region_stat(chrom : String, start : Int32, stop : Int32, name : String | Nil, value : Float64)
• #write_region_zero(chrom : String, start : Int32, stop : Int32, name : String | Nil)
• #write_summary_line(region : String, stat : Depth::Stats::DepthStat)
• #write_summary_total(total : Depth::Stats::DepthStat)

  Optionally call at end to add a total line like mosdepth

• #write_threshold_counts(chrom : String, start : Int32, stop : Int32, name : String | Nil, counts : Array(Int32))
• #write_thresholds_header(thresholds : Array(Int32))

Constructor Detail

Instance Method Detail