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.n_occupied() was implemented differently in hashbits and hashtable #562

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qingpeng opened this issue Jul 23, 2014 · 3 comments · Fixed by #652
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.n_occupied() was implemented differently in hashbits and hashtable #562

qingpeng opened this issue Jul 23, 2014 · 3 comments · Fixed by #652
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@qingpeng
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1.3

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@qingpeng
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as discussed in #429 and #491

Also,in load-graph.py, '--report-total-kmers' option will print .n_occupied() as "Total number of k-mers".
In .info file, .n_unique_kmers() is printed as number of "unique k-mers".
This is confusing. I will look into this.
@qingpeng qingpeng self-assigned this Jul 23, 2014
@mr-c
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mr-c commented Jul 30, 2014

Thanks @qingpeng

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mr-c commented Sep 1, 2014

Any progress?

@mr-c mr-c added this to the 1.2 milestone Sep 1, 2014
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mr-c commented Nov 6, 2014

Upon further review I see that we only count unique k-mers in hashbits. n_occupied merely tells you the number of bins occupied in the first table.

I am going to implement a CountingHash.n_kmers() function and update the scripts to use it instead of n_occupied().

This was referenced Nov 6, 2014
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@ctb ctb closed this as completed in #652 Nov 16, 2014
@mr-c mr-c modified the milestones: 1.3 , 1.3 Dec 19, 2014
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add n_kmers() to CountingHash dib-lab/khmer
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@qingpeng @mr-c