Draw N uniform random sample intervals of length L from assembly hg38, taking into account chromosome lengths

sample_uniform_hg38_intervals.sh

#!/bin/bash

# set -xe
set -e

declare -r samples_required=${1}
declare -r interval_length=${2}

#
# [hg38]
# fetchChromSizes hg38 | grep -v '.*_.*' | sort -k1,1 | grep -v 'chrM' | cut -f2 | tr '\n' ' '
#
declare -a chroms=(chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr2 chr20 chr21 chr22 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrX chrY)
declare -a sizes=(248956422 133797422 135086622 133275309 114364328 107043718 101991189 90338345 83257441 80373285 58617616 242193529 64444167 46709983 50818468 198295559 190214555 181538259 170805979 159345973 145138636 138394717 156040895 57227415)
declare -a cumulative_sizes=()
declare -i accumulated_size=0
for size in ${sizes[@]}; do
  cumulative_sizes+=(${accumulated_size})
  let accumulated_size+=${size}
done
if [[ ${#chroms[@]} -ne ${#sizes[@]} ]] || [[ ${#chroms[@]} -ne ${#cumulative_sizes[@]} ]] || [[ ${#sizes[@]} -ne ${#cumulative_sizes[@]} ]]
then
  echo "Error: Chromosome, sizes, and cumulative sizes arrays are of unequal length"
  exit -1
fi

#
# ref. https://gist.github.com/lovasoa/55550cb561110300ad97398d2cf93214
#
function dichotomic_search {
  min=$1
  max=$2
  command=$3
  while [[ $min < $max ]]
  do
    current=$(( (min + max + 1 ) / 2 ))
    if $command $current
      then min=$current
      else max=$(( current - 1 ))
    fi
  done
  echo $min
}

function is_smaller {
  element=${cumulative_sizes[$2]}
  if [[ ${element} -ge ${1} ]]
    then false
    else true
  fi
}

declare -r highest_index=`expr ${#cumulative_sizes[@]} - 1`
declare -i samples_drawn=0

while [[ ${samples_drawn} -lt ${samples_required} ]]
do
  declare -i absolute_position=${accumulated_size}
  while [[ ${absolute_position} -ge ${accumulated_size} ]] || [[ ${absolute_position} -lt 0 ]]
  do
    (( absolute_position=(RANDOM<<15|RANDOM)<<15|RANDOM ))
  done
  query_index=$(dichotomic_search 0 $highest_index "is_smaller $absolute_position")
  start=$(( ${absolute_position} - ${cumulative_sizes[$query_index]} ))
  stop=$(( ${start} + ${interval_length} ))
  if [[ ${stop} -lt ${sizes[query_index]} ]]
  then
    echo -e "${chroms[$query_index]}\t${start}\t${stop}"
    let samples_drawn+=1
  fi
done

% ./sample_uniform_hg38_intervals.sh 10 10000 | sort-bed -
chr1	37174603	37184603
chr10	14542026	14552026
chr11	32419542	32429542
chr12	64434681	64444681
chr21	8019910	8029910
chr5	174494714	174504714
chr6	34761384	34771384
chr7	3579514	3589514
chrX	26732001	26742001
chrY	46893746	46903746