Merge branch 'master' of https://github.com/maickrau/PartSortBWT

Author: maickrau

README.md

@@ -0,0 +1,31 @@
+## PartSortBWT
+
+Low memory BWT computation. Usage:
+
+```
+std::string input = ...
+std::string output;
+PartSortBWT(input, output); // computes BWT, stores in output
+PartSortBWT(input, input); // computes BWT, stores in the same string and overwrites
+```
+
+The input and output can be the same string. For a real example see [src/main.cpp](src/main.cpp). The input string must end with 0, and all other characters must be between 1-5 representing the alphabet `$NACGT`. Not recommended for strings which have long runs of N's, eg. GRCh38.
+
+### Benchmark
+
+Measured with `/usr/bin/time -v bin/main input_file > /dev/null` using commit [19bb9f4](https://github.com/maickrau/PartSortBWT/commit/19bb9f42b6892d62f7952889ad96fb475c5f35a5) on a laptop.
+
+| Dataset | Size | Time (h:mm:ss) | Memory |
+| --- | --- | --- | --- |
+| CHM13 chr1 hpc | 175 Mbp | 0:00:44 | 291 Mb |
+| CHM13 hpc | 2.1 Gbp | 0:11:35 | 3.6 Gb |
+| CHM13 | 3.1 Gbp | 0:30:03 | 4.9 Gb |
+| Assembly graph hpc | 3.8 Gbp | 0:37:26 | 6.5 Gb |
+| AAAAAA... | 1 Mbp | 0:14:49 | 19 Mb |
+| GRCh38 | 3.3 Gbp | out of memory crash | >12 Gb |
+
+### Method
+
+Classify suffixes according to their first 4 characters. First collect and sort all suffixes starting with AAAA to get the first x characters of the BWT, then suffixes with AAAC to get the next y characters, etc. Repeat for all 4-character prefixes.
+
+Expected memory use for a random DNA string is `input + output + ~0.875n` bytes. If input == output then total memory use is ~1.875n bytes. Less random strings have higher memory use and worst case is one character repeating (eg `NNNNNNNN...`) using ~16n bytes. Expected runtime for a random string is `O(n log^2 n)` and worst case is `O(n^2 log n)`.