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Feature/iterative ordering #4

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58d2aa4
FIXED BUGSSS IN UHS
danflomin Feb 22, 2021
904ea4f
add random ordering
danflomin Feb 23, 2021
ca32615
lolz
danflomin Feb 24, 2021
5634668
checkpoint for runs with yael - checking out to dev-runs3
danflomin Feb 24, 2021
8f1f935
add print for orderings
danflomin Feb 24, 2021
d473d60
checkpoint
danflomin Feb 25, 2021
c5059a2
nothing
danflomin Mar 1, 2021
35d6ac1
nothing
danflomin Mar 3, 2021
948103f
add pruning
danflomin Mar 3, 2021
f93531c
checkpoint
danflomin Mar 8, 2021
9c0e4bb
remove ordering10
danflomin Mar 14, 2021
087a495
add multiple pass over data where each pass opens only 10K files
danflomin Mar 17, 2021
36cf626
add stats and normalization to universal-frequency
danflomin Mar 22, 2021
a7e8afd
add hyperloglog to ordering9 as ordering10. included in stats samplin…
danflomin Mar 22, 2021
e43a387
checkpoint before refactor ordering10 which is not normalized wrt rev…
danflomin Mar 29, 2021
bc737d2
remove ordering10 which had a bug in it
danflomin Mar 29, 2021
6860c36
remove several old iterative orderings
danflomin Mar 29, 2021
43ae8e8
too many tries to fix partitioning - trying it in new branch
danflomin Mar 31, 2021
2c22407
I fixed itttt :))))
danflomin Mar 31, 2021
5001b88
add mechanism for multiple pass to not open many files at once
danflomin Mar 31, 2021
2b3749d
refator
danflomin Mar 31, 2021
1f7ba6b
Merge pull request #1 from danflomin/feature/iterative-ordering-parti…
danflomin Mar 31, 2021
1790197
remove old and not necessary orderings
danflomin Mar 31, 2021
bbe54ca
stable version of partition and IterativeOrdering9_WithCounterNormali…
danflomin Mar 31, 2021
86b335d
add MinimizerCounter for knowing load of each minimizer
danflomin Mar 31, 2021
c5fbfb8
checkpoint for very good version
danflomin Mar 31, 2021
04c4132
remove IterativeOrdering9_WithCounterNormalized.java, it is contained…
danflomin Mar 31, 2021
079b2ef
change name to IterativeOrdering - this is the main product
danflomin Mar 31, 2021
67b8f53
checkpoint before transforming IOrderingPP to abstract class
danflomin Apr 2, 2021
71c63fa
remove some
danflomin Apr 2, 2021
88c3f8b
refactor OrderingBase and subclasses
danflomin Apr 3, 2021
3136929
remove initStats from UHSFrequencySignatureOrdering
danflomin Apr 3, 2021
8c416b6
lots and lots
danflomin Apr 3, 2021
561da21
remove UHSSignatureOrdering.java
danflomin Apr 3, 2021
7469ac4
checked that orderings run succesfully, didn;t check products
danflomin Apr 3, 2021
58c9576
lalala
danflomin Apr 4, 2021
a9dfd5e
checkpoint this stuff and move to new dumbo idea
danflomin Apr 12, 2021
3e0569c
fix bin size counter
danflomin Apr 25, 2021
cc70f5d
remove read len requirement from IterativeOrdering and BinSizeCounter
danflomin Apr 27, 2021
2d94e46
remove iterative ordering 2 which was meant for frequency optimization
danflomin Apr 27, 2021
fd82c12
Merge pull request #2 from danflomin/feature/iterative-ordering-for-freq
danflomin Apr 27, 2021
3203036
Merge pull request #3 from danflomin/feature/iterative-ordering-cardi…
danflomin Apr 27, 2021
5b84616
la lal al a
danflomin Apr 27, 2021
7463a61
cloned to new directory because of intellij problems
danflomin Apr 27, 2021
dffa814
good version
danflomin Jun 9, 2021
a3e641b
removed several unnecessary files
danflomin Jul 15, 2021
aeef1aa
fixed removal of frequency
danflomin Jul 15, 2021
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -19,5 +19,7 @@
*.tar.gz
*.rar

.idea*

# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*
12 changes: 12 additions & 0 deletions msp.iml
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@@ -0,0 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<module type="JAVA_MODULE" version="4">
<component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_9" inherit-compiler-output="true">
<exclude-output />
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
</content>
<orderEntry type="inheritedJdk" />
<orderEntry type="sourceFolder" forTests="false" />
<orderEntry type="library" name="hll-1.6.0-jar-with-dependencies" level="project" />
</component>
</module>
2 changes: 1 addition & 1 deletion src/META-INF/MANIFEST.MF
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
Manifest-Version: 1.0
Main-Class: buildgraph.BuildDeBruijnGraph
Main-Class: dumbo.OrderingOptimizer

190 changes: 0 additions & 190 deletions src/buildgraph/BuildDeBruijnGraph.java
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78 changes: 0 additions & 78 deletions src/buildgraph/Kmer64.java
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