sed-i"s/^.{${barcodeadjust}}//"${barcodefile}#Trim the first n characters from the beginning of the sequence and quality
elif[[ 0 -gt$barcodeadjust]];then
As=`printf'%0.sA'$(seq 1 $(($barcodeadjust*-1)))`
sed-i"s/^/$As/"${barcodefile}#Trim the first n characters from the beginning of the quality
fi
fi
##########
@@ -772,40 +759,32 @@ fi
#set up .lock file
if[[!-f$lockfile]];then
echo"creating .lock file"
echo 0 >$lockfile
echo 1 >$lockfile
lock=`cat$lockfile`
else
#check if jobs running (check value in .lock file)
#check if jobs are running (check value in .lock file)
echo"checking .lock file"
lock=`cat$lockfile`
if[[$lock-le 0 ]];then
echo" call accepted: no other cellranger jobs running"
lock=1
if[[$setup==false]];then
echo$lock>$lockfile
fi
else
if[[-f$lastcallfile]];then
echo" total of $lock cellranger ${cellrangerversion} jobs already running in ${cellrangerpath} with technology $lastcall"
echo" total of $lock cellranger ${cellrangerversion} jobs are already running in ${cellrangerpath} with barcode length (${lastcall_b}), UMI length (${lastcall_u}), and whitelist barcodes (${lastcall_p})"
#check if a custom barcode is used for a run (which cannot be run in parallel)
if[[$lastcall=="custom"]];then
echo"Error: cellranger is currently running with a custom barcode list"
echo"other jobs cannot be run until the current job is complete"
echo"remove $lockfile if $lastcall jobs have completed or aborted"
