samtools version 0.1.19 to samtools version 1.2 (Samtools view conversion)

Question

[startup_biostar]

I have a samtools view statement inside a bioinformatics tool which is older version.

samtools view -X -q 1 -F 1540 bamfile.bam

Now while running this tool in 1.2 version, it throws me an error

Error: view: invalid option -- 'X'

As per the help -X is for

-X --> output FLAG in string (samtools-C specific)

So how to convert this particular statement?

I know that a possible way is to install the same version of samtools. But I would like to know what does that -X do and how can it be converted?

Thanks

Answer 1

[Devon Ryan]

That option was removed and will likely never be replaced. There is no conversion.

The -X option took the numeric flag and changed it to be a string. In theory that might have been simpler for a person to parse...but it was rarely used.