Refactoring VariantContextComparator #1629
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* Responding to my own pr comments on #1593 * doing some refactoring to use the Comparator.comparing API * adding a few more tests
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@cmnbroad Could you take a look at this, it ended up being more new code than I meant it to be so it probably needs a second pair of eyes. |
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blocked because of #1637 |
vruano
reviewed
Jan 29, 2023
| private final Comparator<VariantContext> internalComparator; | ||
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| private static Comparator<VariantContext> makeComparator(final Map<String, Integer> contigIndexLookup) { | ||
| return Comparator.comparingInt((VariantContext vc) -> contigIndexLookup.get(vc.getContig())) |
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Since you are using a lambda to determine the index given the contig names perhaps that is what you should compose in the constructors:
If the constructor param is a SAMSeqDict then (x) -> dict.getRecord(x).getIndex().
If the constructor param is a List then you create that Map.
Also you can add here the NPE capture into a IAE (or whatever) for missing contigs.
| private static class SortedUniquedElementsComparator<T extends Comparable<T>> implements Comparator<Collection<T>>{ | ||
| @Override | ||
| public int compare(final Collection<T> o1, final Collection<T> o2) { | ||
| final Iterator<T> left = new TreeSet<>(o1).iterator(); |
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Perhaps is worth to add trivial cases to avoid TreeSet constructons since quite often alt-alleles list are just 1 in length?
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@clintval I might have gone a bit overboard on refactoring. I really hate how normal comparators are written and like to rewrite them as the newer Comparator.comparing() chains so I did that.
It's great that you added tests, I ended up condensing them into a single test case with a dataprovider and a few additional use cases. I never would have bothered having any if you hadn't mad them in the first place though!