minimap2
Klib
minimap2  Klib  

1  23  
0  4,064  
    
1.8  5.0  
over 2 years ago  22 days ago  
C  C  
GNU General Public License v3.0 or later  MIT License 
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minimap2

sqzlib  kseq compatible DNA fastA/Q encoding and compression library
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 bwamem2 in my github, or you can patch them yourself with the included patches.
Klib

Factor is faster than Zig
In my example the table stores the hash codes themselves instead of the keys (because the hash function is invertible)
Oh, I see, right. If determining the home bucket is trivial, then the backshifting method is great. The issue is just that it’s not as much of a generalpurpose solution as it may initially seem.
“With a different algorithm (Robin Hood or bidirectional linear probing), the load factor can be kept well over 90% with good performance, as the benchmarks in the same repo demonstrate.”
I’ve seen the 90% claim made several times in literature on Robin Hood hash tables. In my experience, the claim is a bit exaggerated, although I suppose it depends on what our idea of “good performance” is. See these benchmarks, which again go up to a maximum load factor of 0.95 (Although boost and Absl forcibly grow/rehash at 0.850.9):
https://strongstarlight4ea0ed.netlify.app/
Tsl, Martinus, and CC are all Robin Hood tables (https://github.com/Tessil/robinmap, https://github.com/martinus/robinhoodhashing, and https://github.com/JacksonAllan/CC, respectively). Absl and Boost are the wellknown SIMDbased hash tables. Khash (https://github.com/attractivechaos/klib/blob/master/khash.h) is, I think, an ordinary openaddressing table using quadratic probing. Fastmap is a new, yettobepublished design that is fundamentally similar to bytell (https://www.youtube.com/watch?v=M2fKMP47slQ) but also incorporates some aspects of the aforementioned SIMD maps (it caches a 4bit fragment of the hash code to avoid most key comparisons).
As you can see, all the Robin Hood maps spike upwards dramatically as the load factor gets high, becoming as much as 56 times slower at 0.95 vs 0.5 in one of the benchmarks (uint64_t key, 256bit struct value: Total time to erase 1000 existing elements with N elements in map). Only the SIMD maps (with Boost being the better performer) and Fastmap appear mostly immune to load factor in all benchmarks, although the SIMD maps do  I believe  use tombstones for deletion.
I’ve only read briefly about bidirectional linear probing – never experimented with it.
 A simple hash table in C

So what's the best data structures and algorithms library for C?
It could be that the cost of the function calls, either directly or via a pointer, is drowned out by the cost of the one or more cache misses inevitably invoked with every hash table lookup. But I don't want to say too much before I've finished my benchmarking project and published the results. So let me just caution against laserfocusing on whether the comparator and hash function are/can be inlined. For example stb_ds uses a hardcoded hash function that presumably gets inlined, but in my benchmarking (again, I'll publish it here in coming weeks) shows it to be generally a poor performer (in comparison to not just CC, the current version of which doesn't necessarily inline those functions, but also STC, khash, and the C++ Robin Hood hash tables I tested).

Generic dynamic array in 60 lines of C
Not an entirely uncommon idea. I've written one.
There's also a wellknown one here, in klib: https://github.com/attractivechaos/klib/blob/master/kvec.h
 C_dictionary: A simple dynamically typed and sized hashmap in C  feedback welcome
 Inside boost::unordered_flat_map

The New Ghostscript PDF Interpreter
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
 C LIBRARY

boost::unordered map is a new king of data structures
Unordered hash map shootout CMAP = https://github.com/tylov/STC KMAP = https://github.com/attractivechaos/klib PMAP = https://github.com/greg7mdp/parallelhashmap FMAP = https://github.com/skarupke/flat_hash_map RMAP = https://github.com/martinus/robinhoodhashing HMAP = https://github.com/Tessil/hopscotchmap TMAP = https://github.com/Tessil/robinmap UMAP = std::unordered_map Usage: shootout [nmillion=40 keybits=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
 C++ containers but in C
What are some alternatives?
bwamem2  The next version of bwamem
stb  stb singlefile public domain libraries for C/C++
bwamem2  The next version of bwamem
Better String  The Better String Library
seqstats  Quick summary statistics on fasta/fastq(.gz) files
Better Enums  C++ compiletime enum to string, iteration, in a single header file
sqzlib  Blocked bases fastX encoding and compression
ZXing  ZXing ("Zebra Crossing") barcode scanning library for Java, Android
ZLib  A massively spiffy yet delicately unobtrusive compression library.
HTTP Parser  http request/response parser for c
Cppcheck  static analysis of C/C++ code
ZBar  Clone of the mercurial repository http://zbar.hg.sourceforge.net:8000/hgroot/zbar/zbar