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Figure out what to do with the reverse complements #2

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dkoslicki opened this issue Jul 31, 2018 · 2 comments
Closed

Figure out what to do with the reverse complements #2

dkoslicki opened this issue Jul 31, 2018 · 2 comments

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@dkoslicki
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Add canonical kmers to the sketch? Or just standard kmers? Add canonical/std kmers to the tree? To the prefilter? For prefix searches?
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
start working on diagnosing #20 which turns out to involve #2 as well…
26a9561 
…. Initial commit to add files. Scratch work, mainly for my local efforts as directories are hard coded.
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
add ground truth containment indicies for #2 and #20
3080025
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
might have found the issue with the bloom filter. committing to track…
0ca50b7 
… changes. #2 and #20
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
almost, but for larger ranges, this is still an issue. #2 and #20
cccd5bb
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
problem really is with the bloom filter. Remove it everywhere, and pr…
bf01bf3 
…oblems in #2 and #20 go away
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
yup yup, remove the BF, and while the performance is terrible wrt tim…
1ccf64f 
…e, the results are accurate. #2 and #20
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
ok, well, at least it works, but only if you rip out the bloom filter…
4f6378f 
… altogether, and don't break if you don't see a TST match for a shorter kmer size. #2 and #20. Calling it a night
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
ok, one last try: prefixes of reverse complements are suffixes of the…
e6a1a3e 
… original (revcomped), realized this is actually issue #19 #20 and #2. Including break for now in StreamingQuery... line 261
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
leaving it as pass for now in StreamingQuery... line 261-262. This ap…
0702d2a 
…pears to resolve the issue, but really need to think better about not adding *all the things* to the TST and BF. #2 #20 #19
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
forgot to increase BF size. #2 #20 #19
a49980f
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
added a last couple of notes for my future reference #2 #20 #19
f7bee92
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
commit output with no BF for checking. #2 #20 #19
0161b06
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
ok, bug sufficiently squashed for now, just code cleanup remains. See #2
b7d4cb7 
 #20 #19
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
code cleanup, prepping for incorporation into master #2 #20 #19
cf64b7a
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
create new branch that will nuke all the non-essential things to merg…
4c53757 
…e to master. #2 #19 #20
dkoslicki added a commit that referenced this issue Mar 18, 2020
@dkoslicki
remove all unecessary files before merge to master #2 #19 #20
13f3fd6
dkoslicki referenced this issue Mar 19, 2020
@dkoslicki
tests still not passing, will need to investigate more...
516ceae
dkoslicki added a commit that referenced this issue Mar 19, 2020
@dkoslicki
Merge branch 'kmer_range_issue_to_merge' addresses #2 #20 and #19
c8c91f4
@dkoslicki
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This is addressed in c8c91f4, but leaving open until we get a more complete testing environment open as per #14 as only checked with local testing.

@dkoslicki dkoslicki mentioned this issue Mar 19, 2020
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dkoslicki added a commit that referenced this issue Mar 19, 2020
@dkoslicki
make sure to add modifications to TST to the StreamingQueryDNADatabas…
115dec3 
…e.py as well #2 #20 #19
dkoslicki added a commit that referenced this issue Mar 20, 2020
@dkoslicki
Well, this is the point of testing, something is still up with the re…
51494e0 
…verse complements: seq2 and seq4 should return 1 all the way through, yet they don't. #14 #2
dkoslicki added a commit that referenced this issue Mar 20, 2020
@dkoslicki
simple enough fix! Revcomps *are* handled properly, just wasn't handl…
69db213 
…ing non-completely full sketches properly. #14 #2
@dkoslicki
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Closing, since solution is: Sketches contain k-mers, query, bloom filter, and TST all contain rev-comps.

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@dkoslicki