migrates conversion step to Perl while allowing special characters in Phred scores (da113d45) · Commits · github_fork / Universc

launch_universc.sh

+3 −2

Original line number	Diff line number	Diff line
		@@ -3653,7 +3653,7 @@ else
		if [[ $barcodeadjust -gt 0 ]]; then
		for convFile in "${convFiles[@]}"; do
		echo " handling $convFile ..."
		perl -pni -e "s/^.{${barcodeadjust}}//g unless (/^[@+]/)" $convFile #Trim the first n characters from the beginning of the sequence and quality
		perl -pni -e "s/^.{${barcodeadjust}}//g if ($. % 2 == 0)" $convFile #Trim the first n characters from the beginning of the sequence and quality
		echo " ${convFile} adjusted"
		done
		elif [[ 0 -gt $barcodeadjust ]]; then
		@@ -3661,7 +3661,8 @@ else
		echo " handling $convFile ..."
		toS=`printf '%0.sA' $(seq 1 $(($barcodeadjust * - 1)))`
		toQ=`printf '%0.sI' $(seq 1 $(($barcodeadjust * - 1)))`
		perl -pni -e "s/^/$toS/g unless (/^[@+]/)" $convFile #Trim the first n characters from the beginning of the sequence and quality
		perl -pni -e "s/^/$toS/g if ($. % 4 == 2)" $convFile #Trim the first n characters from the beginning of the sequence
		perl -pni -e "s/^/$toQ/g if ($. % 4 == 0)" $convFile #Trim the first n characters from the beginning of the quality
		echo " ${convFile} adjusted"
		done
		fi