A tool to generate toy random sequences. For instance, these command can be used to generate toy sequences for kreeq:
./build/bin/randseq --verbose -l 10000 --gc-content 0.2 --mutation-rate 0.01 --average-read-length 50 --read-coverage 50
kreeq validate -f referenceError.fasta -r reads.fastq -o test.bed
awk 'NR==FNR{a[$1$2]=1;next}{if (a[$1$2] == 1) {b=0} else {b=1}; printf $0"\t"b"\n";}' errors.bed test.bed > test.gt.bed
Similarly, this can be used to first convert a kwig to bed and then add ground truth:
./build/bin/randseq --verbose -l 10000 --gc-content 0.2 --mutation-rate 0.01 --average-read-length 50 --read-coverage 50
kreeq validate -f referenceError.fasta -r reads.fastq -o test.kwig
awk 'NR>1 {if ($1 ~ /^f/) {match($2, /chrom=(.*)/, h); match($3, /start=(.*)/, s); pos = s[1]} else {printf h[1]"\t"pos++"\t"$0"\n"}}' test.kwig > test.bed
awk 'NR==FNR{a[$1$2]=1;next}{if (a[$1$2] == 1) {b=0} else {b=1}; printf $0"\t"b"\n";}' errors.vcf test.bed > test.gt.bed