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update disbamer.sh to this:
read -r cigarD <<< "$(echo "$bamdata" | awk '{print $6}')" cigArr=( $(grep -Eo '[[:digit:]]+|[^[:digit:]]+' <<<"$cigarD") ) cigCount="${#cigArr[@]}" echo cigar " |- elements: $(( cigCount / 2 )) -| : " "${cigarD:0:50}" "...." "${cigarD:$(($ciglen-20)):20}." # cigar
read -r seqD <<< "$(echo "$bamdata" | awk '{print $10}')" echo sequence "|- bases: ${#seqD} -| : " "${seqD:0:50}" ".... " "${seqD:$((${#seqD}-20)):20}." # ${::} substring ${#} length of string var
The text was updated successfully, but these errors were encountered:
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update disbamer.sh to this:
read -r cigarD <<< "$(echo "$bamdata" | awk '{print $6}')"$(( cigCount / 2 )) -| : " "$ {cigarD:0:50}" "...." "${cigarD:$(($ciglen-20)):20}." # cigar
cigArr=( $(grep -Eo '[[:digit:]]+|[^[:digit:]]+' <<<"$cigarD") )
cigCount="${#cigArr[@]}"
echo cigar " |- elements:
removed length ${ciglen}, changed form byte length to number of cigar elements.
read -r seqD <<< "$(echo "$bamdata" | awk '{print $10}')"
echo sequence "|- bases: ${#seqD} -| : " "${seqD:0:50}" ".... " "${seqD:$((${#seqD}-20)):20}." # ${::} substring ${#} length of string var
echo "check_"$seqD"_check"
The text was updated successfully, but these errors were encountered: