primer3-org / primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
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ntthal set defaults are different than ntthal usage information defaults #79

Open emmcauley opened 1 month ago

emmcauley commented 1 month ago

In primer3 release 2.6.1, I notice that the ntthal usage information provides a default of 0.0 mM for dNTP concentration:

usage = "USAGE: %s OPTIONS oligo\n"
     "-n  dNTP_conc        - concentration of deoxynycleotide triphosphate in mM, by default 0 mM\n"
     "\n"

However, when I check where the default parameters are actually set in set_thal_default_args, it looks like the default for dNTP concentration is actually 0.8 mM. set_thal_default_args is called on this line:

set_thal_default_args(thal_args *a)
{
   memset(a, 0, sizeof(*a));
   a->type = thal_any; /* thal_alignment_type THAL_ANY */
   a->maxLoop = MAX_LOOP;
   a->mv = 50; /* mM */
   a->dv = 0.0; /* mM */
   a->dntp = 0.8; /* mM */
   a->dna_conc = 50; /* nM */
   a->temp = TEMP_KELVIN; /* Kelvin */
   a->dimer = 1; /* by default dimer structure is calculated */
}

Happy to open a PR to change the usage information if that would be helpful. Thanks!