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Commits on Dec 7, 2020

• Fix bug when runningGSAlign

  

  Andrea Talenti

  committed
  870062b

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• When running GSAlign use whole-genome vs whole-genome

  

  Andrea Talenti

  committed
  8d92d5d

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• Fix far GSAlign identity threshold

  

  Andrea Talenti

  committed
  5e2b02f

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• Fix far command for GSAlign

  

  Andrea Talenti

  committed
  b3bee3a

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• Update version number in manifest

  

  Andrea Talenti

  committed
  61f59b2

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• Better resource handling on single machine

  

  Andrea Talenti

  committed
  e03a970

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• Add last-split to processing of alignments

  

  Andrea Talenti

  committed
  3168601

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• Add last-postmask following lastal

  

  Andrea Talenti

  committed
  403a232

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• Correct naming issue in last_train process

  

  Andrea Talenti

  committed
  c0462aa

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• Correct missing type assignments of input for last_train

  

  Andrea Talenti

  committed
  213601a

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• Fix minor bug in resources allocation for near last alignments

  

  Andrea Talenti

  committed
  0a501a0

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• Add last training matrix

  

  Andrea Talenti

  committed
  5b7bdb9

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Commits on Dec 4, 2020

• Make a single lastDB for the source genome

  

  Andrea Talenti

  committed
  03afa89

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• Fix README.md link

  

  Andrea Talenti

  committed
  c7aae85

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• Better readme describing the input genomes

  

  Andrea Talenti

  committed
  c92506b

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• Clean up code

  

  Andrea Talenti

  committed
  ae441bb

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• Change GSAlign so that generates a general index only once, then uses it in all alignments

  

  Andrea Talenti

  committed
  07dce04

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• Fix preventin run of blat when one sequence in original fasta

  

  Andrea Talenti

  committed
  ba2386b

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• Further fixes to splitting when running GSAlign

  

  Andrea Talenti

  committed
  75ebf59

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Commits on Dec 3, 2020

• Add support for large genomes >4Gb

  

  Andrea Talenti

  committed
  df955e5

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• Expand full genome as source also to GSAlign

  

  Andrea Talenti

  committed
  e1188f6

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• Blat alignments use complete genome as source, instead of split one

  

  Andrea Talenti

  committed
  fbbfdae

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Commits on Dec 2, 2020

• Fix a bug not checking the aligner when splitting

  

  Andrea Talenti

  committed
  e65b9f2

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• Add chunking by sequence when running blat alignments

  

  Andrea Talenti

  committed
  0edceeb

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• Tidy the code from old commentd pieces

  

  Andrea Talenti

  committed
  23723fe

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• Fix typo in logging

  

  Andrea Talenti

  committed
  a9c20a8

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• Fix typo with chaining using custom parameters

  

  Andrea Talenti

  committed
  63bddf5

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• Separate source and target 2bit generation

  

  Andrea Talenti

  committed
  e83c919

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Commits on Dec 1, 2020

• Rename WORKER to ALIGNER tfor clarity

  

  Andrea Talenti

  committed
  65bff12

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• Increase memory for last alignments

  

  Andrea Talenti

  committed
  98fe8a3

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• Further bug fixes in handling chunking of source and target genomes

  

  Andrea Talenti

  committed
  11f4fac

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• Fix issue in splitting of sequences

  

  Andrea Talenti

  committed
  f09099a

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Commits on Nov 27, 2020

• Separate preprocessing stages in a separate sub-workflow

  

  Andrea Talenti

  committed
  77dfd00

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• Add longer time limit for conda env creation

  

  Andrea Talenti

  committed
  b32ed11

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Commits on Nov 26, 2020

• Add improved help function

  

  Andrea Talenti

  committed
  ab390a8

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