class Depth::Config

Defined in:

depth/config.cr

Instance Method Summary

Instance Method Detail

def bed_path : String | Nil #

def by : String #

def by=(by : String) #

def chrom : String #

def chrom=(chrom : String) #

def d4=(d4 : Bool) #

def d4? : Bool #

def exclude_flag : UInt16 #

def exclude_flag=(exclude_flag : UInt16) #

def fast_mode=(fast_mode : Bool) #

def fast_mode? : Bool #

def fasta : String #

def fasta=(fasta : String) #

def fragment_mode=(fragment_mode : Bool) #

def fragment_mode? : Bool #

def has_quantize? : Bool #

def has_regions? : Bool #

def has_thresholds? : Bool #

def include_flag : UInt16 #

def include_flag=(include_flag : UInt16) #

def mapq : Int32 #

def mapq=(mapq : Int32) #

def max_frag_len : Int32 #

def max_frag_len=(max_frag_len : Int32) #

def min_frag_len : Int32 #

def min_frag_len=(min_frag_len : Int32) #

def mos_style=(mos_style : Bool) #

When true, use mosdepth-compatible names (mosdepth.); otherwise mopdepth.


def mos_style? : Bool #

When true, use mosdepth-compatible names (mosdepth.); otherwise mopdepth.


def no_per_base=(no_per_base : Bool) #

def no_per_base? : Bool #

def path : String #

def path=(path : String) #

def prefix : String #

def prefix=(prefix : String) #

def quantize : String #

def quantize=(quantize : String) #

def quantize_args : Array(Int64) #

def read_groups_str : String #

def read_groups_str=(read_groups_str : String) #

def threads : Int32 #

def threads=(threads : Int32) #

def threshold_values : Array(Int32) #

def thresholds : Array(Int32) #

def thresholds=(thresholds : Array(Int32)) #

def thresholds_str : String #

def thresholds_str=(thresholds_str : String) #

def to_options : Core::Options #

def use_d4? : Bool #

def use_median=(use_median : Bool) #

def use_median? : Bool #

def validate! #

def window_size : Int32 #