Mark duplicates in files with many contigs #361
Merged
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This is a resolution to #326 and also something we observed internally (maxplanck-ie/snakepipes#233 ) where markdup is limited to files with <=16383 contigs. This PR modifies the size of the structures such that all BAM files should be supported, regardless of the number of contigs/scaffolds.
In my tests this produces identical results on files already supported by
sambamba markdup
, while requiring a small (10-20% peak) increase in RAM. There's no appreciable run-time difference that I've seen.