jm + bam   1

Faster BAM Sorting with SAMtools and RocksDB
Now this is really really clever. Heap-merging a heavyweight genomics format, using RocksDB to speed it up.
There’s a problem with the single-pass merge described above when the number of intermediate files, N/R, is large. Merging the sorted intermediate files in limited memory requires constantly reading little bits from all those files, incurring a lot of disk seeks on rotating drives. In fact, at some point, samtools sort performance becomes effectively bound to disk seeking. [...] In this scenario, samtools rocksort can sort the same data in much less time, using no more memory, by invoking RocksDB’s background compaction capabilities. With a few extra lines of code we configure RocksDB so that, while we’re still in the process of loading the BAM data, it runs additional background threads to merge batches of existing sorted temporary files into fewer, larger, sorted files. Just like the final merge, each background compaction requires only a modest amount of working memory.


(via the RocksDB facebook group)
rocksdb  algorithms  sorting  leveldb  bam  samtools  merging  heaps  compaction 
may 2014 by jm

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