fill-tags issue for specific sample name

[huangl07]

hello，

I have a vcf file， which sample name is like “A1”，“C1”；

when I using the filter-tag plugins，it turns out error for group files，maybe you could rewrite the check code

/mnt/lustre/users/sanger-dev/app/bioinfo/dna/bcftools-1.17/bcftools +fill-tags --threads 8 -Oz -o pop.hwe.vcf.gz /mnt/lustre/sanger-dev_workspaceDnaEvolutionV2/20230530/Basic_FX2023022000012_16sample_yxy_2ezr/VcfPreprocess/output/vcf_filter/loci_filtered.vcf.gz -- -S /mnt/lustre/users/sanger-dev/sg-users/yexiaoya/task/FX2023022000012/16.group -t HWE

Could not parse the file2: C1	C

I have already change the code plugins/fill-tags.c like this

    166                 char  *back=str.s;
    167         char *smpl=strtok(str.s,"\t");
    168                 char *pop_names=strtok(NULL,"\t");
    169                 str.s=back;
    170                 //while(p)
    171                 //{
    172                 //      printf("%s\n",p);
    173                 //      p=strtok(NULL,"\t");
    174                 //}             
    175                 //char *pop_names = str.s + str.l - 1;
    176                 //while ( pop_names >= str.s && isspace(*pop_names) ) pop_names--;
    177                 //if ( pop_names <= str.s ) error("Could not parse the file: %s\n", str.s);
    178         //pop_names[1] = 0;   // trailing spaces
    179                 //while ( pop_names >= str.s && !isspace(*pop_names) ) pop_names--;
    180         //if ( pop_names <= str.s ) error("Could not parse the file1: %s\n", str.s);
    181 
    182         //char *smpl = pop_names++;
    183         //while ( smpl >= str.s && isspace(*smpl) ) smpl--;
    184                 //char *names= str.s++;
    185                 //if ( smpl <= str.s) error("Could not parse the file2: %s\n", str.s);
    186                 //smpl[1] = 0;
    187         //smpl = str.s;

the error is gone！

thank you！

[pd3]

You seem to be using some older version of the plugin? Even though the command line you are showing suggests that you are at the version 1.17, the code there looks quite different from what you commented out: https://github.com/samtools/bcftools/blob/116a87cae219a1e14e5cc0b2c6331749f9a3bd41/plugins/fill-tags.c#L166-L187

If this is not a version mismatch and the environment variable BCFTOOLS_PLUGINS really points to the correct location, it would be helpful to have a small test case to reproduce and debug the error.

[huangl07]

well, I have already check the issue is still exists

[pd3]

We still need a test case to reproduce the problem, unable to proceed without it, sorry.