Missing checks for malloc failures

[iqbal-lab]

eg this in base_species.c

boolean* create_mask(boolean default_value)
{
boolean* mask = malloc(NUM_SPECIES * sizeof(boolean));

Should check afterwards
eg

if (mask==NULL)
{
fail or return error message
}

Ties into bigger picture of improving error handling being passed back to app

[iqbal-lab]

Actually, given the mask is an array of length NUM_SPECIES of booleans, we are basically talking about ~50 bools. Maybe at worst 200 booleans, right? I'd be tempted to do it on the stack. Not a big deal either way. The other option is to change code from

Species get_best_MTBC_species(SpeciesInfo* species_info ){
boolean* mask = create_MTBC_mask();
int species_enum = get_best_hit(species_info->species_covg_info,mask);
Species species = species_enum;
return (species);
}

to

Species get_best_MTBC_species(SpeciesInfo* species_info ){
boolean* mask = create_MTBC_mask();
int species_enum = get_best_hit(species_info->species_covg_info,mask);
free(mask);
Species species = species_enum;
return (species);
}

[iqbal-lab]

OK, in all cases the fix is very simple - leaving this to fix after ECCMOD

[iqbal-lab]

Phelim, is this still open?

[Phelimb]

I think so. Will take a look on dev and fix before merging to master.