Code

Mcall#389

Code

Merged

ANGSD merged 22 commits intomasterANGSD/angsd:masterfrom mcallANGSD/angsd:mcallCopy head branch name to clipboardMar 31, 2021

+813-53

Commits

Commits on Mar 19, 2021

• Added the mcall, this would the a faithfull reimplementation of the -m in bcftools, implemented for comparison purposes

  ANGSD

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  6561c74

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• Added very small test file

  ANGSD

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  c93aa19

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• QS now works

  

  Thorfinn

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  ac17d90

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Commits on Mar 21, 2021

• put in some validation code

  

  Thorfinn

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  dd5222c

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• modified testfile

  ANGSD

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  7885074

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• edits

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  8552cda

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• Copied some code from bam2bcf from bcftools to abcMcall this was done to ensure ordering of alt alleles. This code will like be removed at a later point

  

  Thorfinn

  committed
  5beda8b

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Commits on Mar 23, 2021

• Extracting now works

  

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  a9af0e1

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• Added diallelic

  

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  7909d73

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Commits on Mar 24, 2021

• Multi allelic snpcaller should now work

  

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  e8020cb

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Commits on Mar 25, 2021

• Prior added now

  

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  497ad29

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Commits on Mar 26, 2021

• Qual reporting correctly

  

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  c273b8a

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• Moved some variables to a different scope

  

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  4fd2a76

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Commits on Mar 27, 2021

• Fixed problem with missing data

  

  Thorfinn

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  5290db0

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Commits on Mar 28, 2021

• Added vcfstructure for printing the multiallelic

  ANGSD

  committed
  205ee75

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• First version of the multiallelic genotype caller should now work. Output is still diallelic. Need to think about how to represent things. Maybe just an integer from 0-9 similar to the offset of th…

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Commits on Mar 31, 2021

• Genotype likelihoods are only calculated for sites that are relevant

  

  Thorfinn

  committed
  3f5d964

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• Di allelic version of the multicaller now works with genotype calling also

  

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  committed
  b96a876

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• Included missing assert

  

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  c129692

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• Added missing -lcrypto in linking

  

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  df41884

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• added missing crypto in misc/Makefile

  ANGSD

  committed
  b92eb7e

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• Changed to proper indexing after we have added the multicaller. I think it works now

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  2f43516

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