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Update memory.md for new flag names (#15)
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output-handles instead of bam-handles (applies at least since lima 2.7.1)
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kristinalweber authored Feb 17, 2023
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Expand Up @@ -13,10 +13,10 @@ In this case, memory usage (RES column in top) is approximately the size of the
input, uncompressed.

The maximum concurrent output BAM file handles can be adjusted with
`--bam-handles N`. The default is 500.
`--bam-handles N` or `--output-handles N`. The default is 500.

Examples, how memory usage is affected by `--bam-handles`. Option
`--bam-handles-verbose` is only used to visualize the BAM output file handles.
`--bam-handles-verbose` or `--output-handles-verbose` is only used to visualize the BAM output file handles.
Memory usage reported using [memusg](https://gist.github.com/netj/526585):

$ lima input.bam barcodes.fasta out.bam --same --split-bam --bam-handles 9 --bam-handles-verbose
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