Closed HYan-lei closed 4 years ago
Hi, I want to take the absolute value of the TLEN of each bam read and filters to those between 90 and 150 bp, and I use the following command and get the wrong message, can anyone please give me some suggestions? Thanks.
Haiyan
sambamba view -t 7_JS0022CD050118.dd.bam | awk -F'\t' 'sqrt($9$9) < 150 {print $0}' | awk -F'\t' 'sqrt($9$9) > 90' > 7_JS0022CD050118.frag.nohead
sambamba 0.7.1 by Artem Tarasov and Pjotr Prins (C) 2012-2019 LDC 1.17.0 / DMD v2.087.1 / LLVM8.0.1 / bootstrap LDC - the LLVM D compiler (1.17.0)
sambamba-view: Unexpected '_' when converting from type string to type uint
I think this is fixed by author.
pjotrp
commented
4 years ago
Hi, I want to take the absolute value of the TLEN of each bam read and filters to those between 90 and 150 bp, and I use the following command and get the wrong message, can anyone please give me some suggestions? Thanks.
Haiyan
sambamba view -t 7_JS0022CD050118.dd.bam | awk -F'\t' 'sqrt($9$9) < 150 {print $0}' | awk -F'\t' 'sqrt($9$9) > 90' > 7_JS0022CD050118.frag.nohead
sambamba 0.7.1 by Artem Tarasov and Pjotr Prins (C) 2012-2019 LDC 1.17.0 / DMD v2.087.1 / LLVM8.0.1 / bootstrap LDC - the LLVM D compiler (1.17.0)
sambamba-view: Unexpected '_' when converting from type string to type uint