sqzlib VS Klib

Code reuse is achievable by (mis)using the preprocessor system. It is possible to build a somewhat usable API, even for intrusive data structures. (eg. the linux kernel and klib[1])

I do agree that generics are required for modern programming, but for some, the cost of complexity of modern languages (compared to C) and the importance of compatibility seem to outweigh the benefits.

[1]: http://attractivechaos.github.io/klib

Unordered hash map shootout CMAP = https://github.com/tylov/STC KMAP = https://github.com/attractivechaos/klib PMAP = https://github.com/greg7mdp/parallel-hashmap FMAP = https://github.com/skarupke/flat_hash_map RMAP = https://github.com/martinus/robin-hood-hashing HMAP = https://github.com/Tessil/hopscotch-map TMAP = https://github.com/Tessil/robin-map UMAP = std::unordered_map Usage: shootout [n-million=40 key-bits=25] Random keys are in range [0, 2^25). Seed = 1656617916: T1: Insert/update random keys: KMAP: time: 1.949, size: 15064129, buckets: 33554432, sum: 165525449561381 CMAP: time: 1.649, size: 15064129, buckets: 22145833, sum: 165525449561381 PMAP: time: 2.434, size: 15064129, buckets: 33554431, sum: 165525449561381 FMAP: time: 2.112, size: 15064129, buckets: 33554432, sum: 165525449561381 RMAP: time: 1.708, size: 15064129, buckets: 33554431, sum: 165525449561381 HMAP: time: 2.054, size: 15064129, buckets: 33554432, sum: 165525449561381 TMAP: time: 1.645, size: 15064129, buckets: 33554432, sum: 165525449561381 UMAP: time: 6.313, size: 15064129, buckets: 31160981, sum: 165525449561381 T2: Insert sequential keys, then remove them in same order: KMAP: time: 1.173, size: 0, buckets: 33554432, erased 20000000 CMAP: time: 1.651, size: 0, buckets: 33218751, erased 20000000 PMAP: time: 3.840, size: 0, buckets: 33554431, erased 20000000 FMAP: time: 1.722, size: 0, buckets: 33554432, erased 20000000 RMAP: time: 2.359, size: 0, buckets: 33554431, erased 20000000 HMAP: time: 0.849, size: 0, buckets: 33554432, erased 20000000 TMAP: time: 0.660, size: 0, buckets: 33554432, erased 20000000 UMAP: time: 2.138, size: 0, buckets: 31160981, erased 20000000 T3: Remove random keys: KMAP: time: 1.973, size: 0, buckets: 33554432, erased 23367671 CMAP: time: 2.020, size: 0, buckets: 33218751, erased 23367671 PMAP: time: 2.940, size: 0, buckets: 33554431, erased 23367671 FMAP: time: 1.147, size: 0, buckets: 33554432, erased 23367671 RMAP: time: 1.941, size: 0, buckets: 33554431, erased 23367671 HMAP: time: 1.135, size: 0, buckets: 33554432, erased 23367671 TMAP: time: 1.064, size: 0, buckets: 33554432, erased 23367671 UMAP: time: 5.632, size: 0, buckets: 31160981, erased 23367671 T4: Iterate random keys: KMAP: time: 0.748, size: 23367671, buckets: 33554432, repeats: 8, sum: 4465059465719680 CMAP: time: 0.627, size: 23367671, buckets: 33218751, repeats: 8, sum: 4465059465719680 PMAP: time: 0.680, size: 23367671, buckets: 33554431, repeats: 8, sum: 4465059465719680 FMAP: time: 0.735, size: 23367671, buckets: 33554432, repeats: 8, sum: 4465059465719680 RMAP: time: 0.464, size: 23367671, buckets: 33554431, repeats: 8, sum: 4465059465719680 HMAP: time: 0.719, size: 23367671, buckets: 33554432, repeats: 8, sum: 4465059465719680 TMAP: time: 0.662, size: 23367671, buckets: 33554432, repeats: 8, sum: 4465059465719680 UMAP: time: 6.168, size: 23367671, buckets: 31160981, repeats: 8, sum: 4465059465719680 T5: Lookup random keys: KMAP: time: 0.943, size: 23367671, buckets: 33554432, lookups: 34235332, found: 29040438 CMAP: time: 0.863, size: 23367671, buckets: 33218751, lookups: 34235332, found: 29040438 PMAP: time: 1.635, size: 23367671, buckets: 33554431, lookups: 34235332, found: 29040438 FMAP: time: 0.969, size: 23367671, buckets: 33554432, lookups: 34235332, found: 29040438 RMAP: time: 1.705, size: 23367671, buckets: 33554431, lookups: 34235332, found: 29040438 HMAP: time: 0.712, size: 23367671, buckets: 33554432, lookups: 34235332, found: 29040438 TMAP: time: 0.584, size: 23367671, buckets: 33554432, lookups: 34235332, found: 29040438 UMAP: time: 1.974, size: 23367671, buckets: 31160981, lookups: 34235332, found: 29040438

If you want a generic, extremely high performance implementation. I really recommend khash: https://github.com/attractivechaos/klib/blob/master/khashl.h

Most importantly, sqzlib is fully compatible with klib/kseq.h one of the highest performance fastA/Q parsers. This means that any application that uses kseq.h for fastA/Q parsing, can be easily modified to use sqzlib instead. You can find patched versions of seqstats, minimap2, and bwa-mem2 in my github, or you can patch them yourself with the included patches.

I don;t know if you are aware of khash? It's a very nifty hash table implementation. It is one of the fastest hash table implementations out there. Heavily used in bioinformatics. You said in your post that you are a macro guy, well, you are in for a treat with this library.