Open EricDeveaud opened 1 year ago
Hello,
playing with version 1.1.dev I nioticed that commit https://github.com/KCCG/ClinSV/commit/c20c21a3c604c7b484daf6b66223c994dfbc458e seems to have wrong perl <-> shell syntax escaping
seems to me that line should be.
print OUT "[ -z \"\${readLArr[$outStemSC]}\" ] && readLArr[$outStemSC]=\$(samtools view $projectDir/alignments/$cSample/$cSample.bam chr1:1000000-1100000 | cut -f 10 | awk '{ print length}' | sort -rn | awk '(NR==1){print}' )\n"; instead
print OUT "[ -z \"\${readLArr[$outStemSC]}\" ] && readLArr[$outStemSC]=\$(samtools view $projectDir/alignments/$cSample/$cSample.bam chr1:1000000-1100000 | cut -f 10 | awk '{ print length}' | sort -rn | awk '(NR==1){print}' )\n";
as readLArr is an aray.
what do you think ?
Eric
Hello,
playing with version 1.1.dev I nioticed that commit https://github.com/KCCG/ClinSV/commit/c20c21a3c604c7b484daf6b66223c994dfbc458e seems to have wrong perl <-> shell syntax escaping
seems to me that line should be.
print OUT "[ -z \"\${readLArr[$outStemSC]}\" ] && readLArr[$outStemSC]=\$(samtools view $projectDir/alignments/$cSample/$cSample.bam chr1:1000000-1100000 | cut -f 10 | awk '{ print length}' | sort -rn | awk '(NR==1){print}' )\n";insteadas readLArr is an aray.
what do you think ?
Eric