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A few things for @lgautier and @luizirber to weigh in on --
* the `sourmash_lib.signature` module is badly named; I keep on colliding names with `sig`, etc. I was thinking of renaming it `sigutils`…
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Hi all,
my student @luizirber has implemented a way to search large collections of MinHashes using [Sequence Bloom Trees](http://ivory.idyll.org/blog/2015-sequence-bloom-trees-thoughts.html): see h…
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- [x] Only resize the query mh if we need to (and memoize it)
- [x] Something is wrong with resizing. Try `time python -m search.frontier_search mircea-rm18.0.fa.sig podar 0.1` to see failure.
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https://github.com/dib-lab/sourmash/commit/564f89d319e899fe5220c9644d7984e1b1f9053f
update Estimators class to MinHash
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Is there a way when streaming sequences into sourmash to every now and then "emit" the signature, while the overall process continues? Like peeking at the result.
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Hi, I want to got the top k element with MinHashLSH but failed. For example, I set 'k=3', but I got ('result: ', ['21', '28', '51', '1', '82', '3', '91', '69', '86', '85']), whose length is larger tha…
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When we build a Catlas node using the `create_node()` method, it sets the size of the node to be the sum of the sizes of its children. I am under the impression that the size should stand for the num…
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Hi,
I have full length cDNA nanopore sequencing and would like to use canu to find consesus from these reads and do trimming. Is this something within canu abilities? If so, can I lower read length…
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The released Mash version 1.1.1 fails to build with GCC 7:
```
$ ./configure --with-capnp=/usr
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler def…
satta updated
7 years ago
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As I'm starting to use our HPC, I'm reminded that some filesystems do less well than others at dealing with thousands to millions of tiny little files...
We want something that can be indexed into …