Extract auxiliary tags from BAM file

[sagnikbanerjee15]

Hello,

I wish to extract some fields from a BAM file of B type. For example, jM:B:c,1 jI:B:i,3914,3995. Here is the code I am using:

uint8_t *jI = bam_aux_get(aln,"jI");
printf("\nValue of jI: %hhn", jI);
if(jI != NULL)
{
    char *jI_val = NULL;
    jI_val = bam_aux2Z(jI);
    printf("\njI:%s", jI_val);
}

I know what I am doing is incorrect but I am unsure what to replace it with. Could you please help?

Also, is there detailed documentation about the API?

Thank you.

[daviesrob]

For B tags, use bam_aux_get() followed by bam_auxB_len, then bam_auxB2i or bam_auxB2f depending on type.

[sagnikbanerjee15]

Thanks it worked!