Are you using the latest version of samtools and HTSlib? If not, please specify.
(run samtools --version)
1.19.2
When specifying samtools flags using symbolic strings, samtools doesn't raise an error if an invalid symbolic flag name is used.
E.g. writing samtools view -c -f UMAP myfile.bam (using UMAP instead of the correct UNMAP) silently outputs 0.
Are you using the latest version of samtools and HTSlib? If not, please specify.
(run
samtools --version)1.19.2
When specifying samtools flags using symbolic strings, samtools doesn't raise an error if an invalid symbolic flag name is used.
E.g. writing samtools view -c -f UMAP myfile.bam (using UMAP instead of the correct UNMAP) silently outputs 0.