Code

Feature/iterative ordering#4

Code

Open

danflomin wants to merge 47 commits intodevelopdanflomin/msp:developfrom feature/iterative-orderingdanflomin/msp:feature/iterative-orderingCopy head branch name to clipboard

+1,296-1,546

Commits

Commits on Feb 22, 2021

• FIXED BUGSSS IN UHS

  danflomin

  committed
  58d2aa4

Commits on Feb 23, 2021

• add random ordering

  danflomin

  committed
  904ea4f

Commits on Feb 24, 2021

• lolz

  danflomin

  committed
  ca32615

• checkpoint for runs with yael - checking out to dev-runs3

  danflomin

  committed
  5634668

• add print for orderings

  danflomin

  committed
  8f1f935

Commits on Feb 25, 2021

• checkpoint

  danflomin

  committed
  d473d60

Commits on Mar 1, 2021

• nothing

  danflomin

  committed
  c5059a2

Commits on Mar 3, 2021

• nothing

  danflomin

  committed
  35d6ac1

• add pruning

  danflomin

  committed
  948103f

Commits on Mar 8, 2021

• checkpoint

  danflomin

  committed
  f93531c

Commits on Mar 14, 2021

• remove ordering10

  danflomin

  committed
  9c0e4bb

Commits on Mar 17, 2021

• add multiple pass over data where each pass opens only 10K files

  danflomin

  committed
  087a495

Commits on Mar 22, 2021

• add stats and normalization to universal-frequency

  danflomin

  committed
  36cf626

• add hyperloglog to ordering9 as ordering10. included in stats sampling phase

  danflomin

  committed
  a7e8afd

Commits on Mar 29, 2021

• checkpoint before refactor ordering10 which is not normalized wrt reverse complement

  danflomin

  committed
  e43a387

• remove ordering10 which had a bug in it

  danflomin

  committed
  bc737d2

• remove several old iterative orderings

  danflomin

  committed
  6860c36

Commits on Mar 31, 2021

• too many tries to fix partitioning - trying it in new branch

  danflomin

  committed
  43ae8e8

• I fixed itttt :))))

  danflomin

  committed
  2c22407

• add mechanism for multiple pass to not open many files at once

  danflomin

  committed
  5001b88

• refator

  danflomin

  committed
  2b3749d

• Merge pull request #1 from danflomin/feature/iterative-ordering-partitioninig-fix

  Show description for 1f7ba6b
  danflomin

  authored
  1f7ba6b

• remove old and not necessary orderings

  danflomin

  committed
  1790197

• stable version of partition and IterativeOrdering9_WithCounterNormalized_AndSignature

  danflomin

  committed
  bbe54ca

• add MinimizerCounter for knowing load of each minimizer

  danflomin

  committed
  86b335d

• checkpoint for very good version

  danflomin

  committed
  c5fbfb8

• remove IterativeOrdering9_WithCounterNormalized.java, it is contained in IterativeOrdering9_WithCounterNormalized_AndSignature

  danflomin

  committed
  04c4132

• change name to IterativeOrdering - this is the main product

  danflomin

  committed
  079b2ef

Commits on Apr 2, 2021

• checkpoint before transforming IOrderingPP to abstract class

  danflomin

  committed
  67b8f53

• remove some

  Show description for 71c63fa
  danflomin

  committed
  71c63fa

Commits on Apr 3, 2021

• refactor OrderingBase and subclasses

  danflomin

  committed
  88c3f8b

• remove initStats from UHSFrequencySignatureOrdering

  danflomin

  committed
  3136929

• lots and lots

  danflomin

  committed
  8c416b6

• remove UHSSignatureOrdering.java

  danflomin

  committed
  561da21

• checked that orderings run succesfully, didn;t check products

  danflomin

  committed
  7469ac4

Commits on Apr 4, 2021

• lalala

  danflomin

  committed
  58c9576

Commits on Apr 12, 2021

• checkpoint this stuff and move to new dumbo idea

  danflomin

  committed
  a9dfd5e

Commits on Apr 25, 2021

• fix bin size counter

  Show description for 3e0569c
  danflomin

  committed
  3e0569c

Commits on Apr 27, 2021

• remove read len requirement from IterativeOrdering and BinSizeCounter

  Show description for cc70f5d
  danflomin

  committed
  cc70f5d

• remove iterative ordering 2 which was meant for frequency optimization

  danflomin

  committed
  2d94e46

• Merge pull request #2 from danflomin/feature/iterative-ordering-for-freq

  Show description for fd82c12
  danflomin

  authored
  fd82c12

• Merge pull request #3 from danflomin/feature/iterative-ordering-cardinality-counter

  Show description for 3203036
  danflomin

  authored
  3203036

• la lal al a

  danflomin

  committed
  5b84616

• cloned to new directory because of intellij problems

  Show description for 7463a61
  danflomin

  committed
  7463a61

Commits on Jun 9, 2021

• good version

  danflomin

  committed
  dffa814

Commits on Jul 15, 2021

• removed several unnecessary files

  danflomin

  committed
  a3e641b

• fixed removal of frequency

  danflomin

  committed
  aeef1aa