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Commits on Sep 2, 2023

• Updating database and hdf5 libraries for seqcode core

  

  Shaun Mahony

  committed
  4c5906b

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Commits on May 25, 2023

• Merge pull request #3 from yztxwd/master

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  shaunmahony

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  b080986

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• Adjust ExptConfig arguments

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  yztxwd

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  8a4c683

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Commits on May 24, 2023

• fix: bug the frag size freq doesn't increment by weight

  yztxwd

  committed
  620f4e6

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• fix: bug that causes inconsistent fragment size distribution

  yztxwd

  committed
  0e8f19e

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• add: junit tests for HDF5 hit loader

  yztxwd

  committed
  f0a9238

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• remove: unnecessary main functions

  yztxwd

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  1e31050

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• clean code

  yztxwd

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  7a8b845

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• Load reference array into memory to increase search speed

  yztxwd

  committed
  a4b76f7

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• minor change

  yztxwd

  committed
  eb93785

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• Some changes to save memory

  yztxwd

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  46d20f9

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• Minor bug fix: close memory space after write/read to release resource

  yztxwd

  committed
  905641d

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• Now HDF5HitCache can load hits directly from HDF5 file

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  yztxwd

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  5ae2211

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• Update other class associated with experimentManager to fit HDF5

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  yztxwd

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Commits on May 23, 2023

• Minor change

  yztxwd

  committed
  b82b3bf

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• add HitCacheInterface and other updates

  yztxwd

  committed
  9c312ff

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• minor fix

  yztxwd

  committed
  acea19b

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• Add readHHI to store the read info

  yztxwd

  committed
  af58939

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• minor fix

  yztxwd

  committed
  d90e53c

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• minor fix

  yztxwd

  committed
  913af38

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• minor change

  yztxwd

  committed
  6095dbd

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• Minor fix

  yztxwd

  committed
  427ba7b

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• New class for HDF5 hierarchical data stucture

  yztxwd

  committed
  635d6af

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Commits on Feb 16, 2023

• Merge pull request #2 from yztxwd/upstream_master

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  shaunmahony

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Commits on Feb 6, 2023

• Merge branch 'feat-fragmentMidpoint' into upstream_master

  yztxwd

  committed
  614c7d6

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• add: print # hitpairs summary in ExperimentManager

  yztxwd

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  53ba0d6

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• Add sortMid option

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  yztxwd

  committed
  01048d4

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• add: methods on getting strandedPairCounts

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  yztxwd

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  f2ba0dd

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• add: pairMid array in HitCache, populateArrays by parMid

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  yztxwd

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  376c92a

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• Add getFragSizeFrequency method to prepare data for GMM

  yztxwd

  committed
  e6d87a1

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Commits on May 18, 2022

• Adding support for TAIR10

  shaunmahony

  committed
  db04b02

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Commits on Dec 22, 2020

• Adding dm6 genome

  shaunmahony

  committed
  6c6b87f

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Commits on Aug 20, 2020

• Adding properties for additional genomes

  shaunmahony

  committed
  fb4a0a0

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Commits on Jul 9, 2020

• Fixing handling of non-uniquely mapped reads when loading from SAM/BAM

  shaunmahony

  committed
  f5bc9ea

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Commits on Jul 4, 2020

• Updating figure saving

  shaunmahony

  committed
  cdc2d13

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