Memory optimisations #15
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added 23 commits
May 27, 2016 17:08
This assert helps to validate that the sequences outputted are the same in size.
When filtering VCF all records were kept in memory. This leads to huge memory consumption (~10G for 5Mb genome). Now, if *out_vcf* is specified for *VariantSet.filter_vcf* then as soon as record in filtered, it is written to the file. Thus reducing memory footprint, which is mostly python stuff now.
Some features have been disabled, but otherwise comporable result is returned from old version, but more memory friendly.
calculation. Distance matrix calculation is going to be done in a separate module.
ParallelVCFReader can now be found and used to travers multiple VCF readers one position at a time.
sample-gaps filtering.
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I have reworked the filtering and vcf2fasta steps that will allow more efficient memory usage (See #12)
TODO: