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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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downsampling by sambamba with seed #471

Open dulunar opened 3 years ago

dulunar commented 3 years ago

I have checked the source code of sambamba view in view.d file. And I found that there has some codes:

160 subsampling_seed = unpredictableSeed; 161 subsampling_seed <<= 32; 162 subsampling_seed += unpredictableSeed;

I have some questions:

  1. Does it mean that seed doesn't need to be set?
  2. When I set the seed from 1-100, I found that the kept reads number is very different. Sometimes, the difference is an order of magnitude at 10^6.

Please tell us how to ste the seed number. Thanks.

pjotrp commented 3 years ago

There is a command line parameter for setting the seed