Add additional strata to freq dict labels

[mike-w-wilson]

We built functionality to add additional strata to the freq array but did not include the ability to build those strata into the freq index dictionary. This seemed like the simplest way to do this. Additional strata are simply added to the end of the label amr_xx_adj_4.1.0.1. We historicaly have liked to see adj last so I did put a note that we could insert before the last elemnt in sort order. We could also add the functionality to insert the strata into the SORT_ORDER list at a certain index but this requires knowledge of the order and the order could change based on other groupings. For these reasons, I felt it was best (and easiest) to tack it onto the end of the order or before the last element.

[jkgoodrich]

maybe this is a really stupid question, but can we change to just something like this:

def make_freq_index_dict(
    freq_meta: List[Dict[str, str]],
    label_delimiter: str = "_",
    sort_order: Optional[List[str]] = SORT_ORDER,
) -> Dict[str, int]:
    index_dict = {}
    for i, f in enumerate(freq_meta):
        if sort_order and len(set(f.keys()) - set(sort_order)) < 1:
            index_dict[label_delimiter.join([f[g] for g in sorted(f.keys(), key=(lambda x: sort_order.index(x)) if sort_order else None)])] = i

    return index_dict

We could rename it something so that the existing function still exists as is, but I think this is way over complicated for what we need

[KoalaQin]

All the other parts look good, do you want to keep the second solution for now?

[KoalaQin]

I tested Julia's suggestion, but I think you need to put the addtional_strata in the SORT_ORDER now. Julia prefers adj/raw in the end of all the combos.
Also, this code need a minor change:

def make_freq_index_dict(
    freq_meta: List[Dict[str, str]],
    label_delimiter: str = "_",
    sort_order: Optional[List[str]] = SORT_ORDER,
) -> Dict[str, int]:
    index_dict = {}
    for i, f in enumerate(freq_meta):
        if sort_order and (len(f.keys()) - len(sort_order)) < 1:
            index_dict[label_delimiter.join([f[g] for g in sorted(f.keys(), key=(lambda x: sort_order.index(x)) if sort_order else None)])] = i

    return index_dict

[KoalaQin]

Do you need to add additional strata like "gatk_version" in SORT_ORDER

[mike-w-wilson]

Closing this PR as I added Julia's suggestion to another PR #551