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haotianteng / Chiron

A basecaller for Oxford Nanopore Technologies' sequencers
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Multiple fixed (( merging few PRs )) #50

Closed nmiculinic closed 6 years ago

nmiculinic commented 6 years ago

This PR merges following PR and fixes merge conflicts:

48

49

47

nmiculinic commented 6 years ago

Closing since this one has a lot going on

haotianteng commented 6 years ago

yes, it should change to 100, thanks.

On Mon, Apr 30, 2018, 5:40 PM Neven Miculinic notifications@github.com wrote:

@nmiculinic commented on this pull request.

In chiron/chiron_eval.py https://github.com/haotianteng/Chiron/pull/50#discussion_r184925251:

 logits_queue = tf.FIFOQueue(
  • capacity=FLAGS.batch_size * 100,
  • dtypes=[tf.float32, tf.int32, tf.int32],
  • shapes = [logits.shape,logits_index.shape,seq_length.shape]
  • capacity=100 * FLAGS.batch_size,

Actually, this should be waaaay smaller. I'd say 16 is okish. Each queue element is whole batch, thus multiplying by batch size is wrong thing to do

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