using guile like a awk filter in a C program.

[Pierre LINDENBAUM]

Hi all,

I tried to learn guile a few years ago with a side project that went 
nowhere.

I'm now back with guile that I would like to use as a filter, just like 
awk, for my data.
I've got question about the general design of such program.

My program uses a C library ( https://github.com/samtools/htslib ) 
scanning mutations/variants in large VCF files ( 
https://en.wikipedia.org/wiki/Variant_Call_Format ).

A typical C program looks like (pseudo code) ;

        ```
        header = read_header(input);
        variant = new_variant();
        while(read_variant(input,header,variant)) {
                do_something(header,variant)
                }
        dispose_variant(variant)
        dispose_header(header)
        ```

I would like to use guile to filter VCF using a custom user GUILE 
expression/program . So my program would now look like

        ```
        header = read_header(input);
        guile_context = my_initialize_guile(header, argc_argv_user_script)
        variant = new_variant();
        while(read_variant(input,header,variant)) {
                if(!my_guile_test(guile_context,header,variant)) {
                        continue;
                        }
                do_something(header,variant)
                }
        dispose_variant(variant)
        my_dispose_guile(guile_context)
        dispose_header(header)
        ```

and would may be be invoked like:

```
./a.out -e '(and (variant-is-snp? ) (equals? (variant-allele-count) 2))' 
input.vcf > output.vcf
```

where `variant-is-snp` would test if the current variant in the 'while' 
loop is a 'single nucleotide polylmorphism' using `bcf_is_snp` 
https://github.com/samtools/htslib/blob/develop/htslib/vcf.h#L889


So my questions are:

- is it possible to use guile for such task ? More precisely, can I 
compile the guile script just once in `my_initialize_guile` and use it 
in the while loop without having to recompile it.
- furthermore, what's the best practice to include the user's script in 
a larger script that would include the definitions of `variant-is-snp?` 
, `variant-allele-count`, etc...
- is there any implementation that works like this (something like a AWK 
script in guile) ?
- is there any way to make the program stateless ? I mean, any 
invocation of `my_guile_test` would erase the definition of the previous 
variant

Thanks for your answers,

Pierre L