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Multiple k-mer sizes bug #19

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dkoslicki opened this issue Feb 6, 2020 · 2 comments
Closed

Multiple k-mer sizes bug #19

dkoslicki opened this issue Feb 6, 2020 · 2 comments

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@dkoslicki
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Current implementation of multiple k-mer size containment index computation may have some bugs in it as noted here. In particular, training with 30-60-10 and training with 60-60-10 results in different 60-mer containment index values (which it shouldn't).
@dkoslicki dkoslicki mentioned this issue Feb 6, 2020
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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 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
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Closing as some testing is done, and more testing is being implemented in #14

@dkoslicki dkoslicki mentioned this issue Mar 25, 2020
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@dkoslicki