Problem with specifying filtering expression v1.21

[reshu23]

Dear Team,
I am using bcftools 1.21. I have noticed, in this version, I can not use space between filtering expression. For example: when I tried bcftools stats -i 'QUAL>8 && DP>=10', It was not working. When I removed space between QUAL && and DP, It worked. Here is the screen shot: Is it the expected behavior of 1.21.? Thank you.

[pd3]

I suspect you forgot to put the filtering expression in quotes, therefore the program never saw the expression you intended it to execute. The arguments are passed to the program by the shell, so you must make sure the correct things is passed by putting it in quotes

# this works
-i 'DP>10 && QUAL>10'

# this cannot work
-i DP>10 && QUAL>10

[reshu23]

I used with quote like this -i 'DP>10 && QUAL>10' . But it is not working until I am not going to remove space between "0 && Q". And use it like -i 'DP>10&&QUAL>10'. Is it because of this change?: Support multiple semicolon-separated strings when filtering by ID using -i/-e (#2190). For example, -i 'ID="rs123"' now correctly matches rs123;rs456

[pd3]

The spaces are not required. It must be down to a problem of how you are running the program. Are you executing it directly from a command line, or wrapping in a script, or how do you run it? This functionality has been in bcftools for a long time and there was no breaking change. I am unable to reproduce the problem, with any version.

[reshu23]

I am using singularity image from here: https://depot.galaxyproject.org/singularity/

And I just use singularity exec image bcftools stats -i .......

[pd3]

I don't have much experience with singularity myself, but likely the arguments must be escaped somehow. Can you try to create a wrapper script and escape the arguments like this

#!/bin/bash
singularity exec singularity.sif bcftools "$@";

[reshu23]

Thank you. Yes, it is working now in wrapper script as suggested by you.