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Commits on Jan 15, 2021

• Merge changes from dev

  RomainFeron

  committed
  fcbb48d

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• Removed redundant version number in readme

  RomainFeron

  committed
  0529c63

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• Fixed merge conflict

  RomainFeron

  committed
  15f7e29

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• Minor readme update

  RomainFeron

  committed
  3f6e74d

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• Re-activated gene metrics

  RomainFeron

  committed
  40a4e76

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Commits on Mar 11, 2020

• Small README updates, added badges for extra swag

  RomainFeron

  committed
  4e8af7e

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Commits on Mar 10, 2020

• Updated makefile so that env variables are appended instead of overwritten (for conda)

  RomainFeron

  committed
  78a1f19

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• Removed 'CPP' variable in makefile - it was conflicting with the CPP environment variable for C PreProcessor

  RomainFeron

  committed
  f16f5da

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• Cleaned up compilers in makefile after testing packaging for Conda

  RomainFeron

  committed
  97d2140

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• Minor help message update

  RomainFeron

  committed
  2b457e9

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• Removed kpool code, will be moved to its own repository

  RomainFeron

  committed
  f8d5777

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Commits on Feb 27, 2020

• Force rm HTSLIB_CONF_FLAG in makefile for rare cases when the file does not exist before rebuilding

  RomainFeron

  committed
  5690592

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• Enforce using gcc to build htslib (was using g++ in some cases)

  RomainFeron

  committed
  1042b4f

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Commits on Feb 24, 2020

• Fixed make always building objects because mkdir -p updates directory timestamp

  RomainFeron

  committed
  a0add85

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Commits on Feb 23, 2020

• Added htslib autotools output to gitignore

  RomainFeron

  committed
  9ee87f0

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• Updated makefile after PR #2 . Now -j is passed to htslib

  RomainFeron

  committed
  40a3f81

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• Removed autoconf output from htslib (autoconf will be included in makefile)

  RomainFeron

  committed
  3c2cb7a

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• Merge pull request #2 from KamilSJaron/dev

  Show description for 7b17ad3
  RomainFeron

  authored
  7b17ad3

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Commits on Feb 21, 2020

• draft of a makefile that uses more cores for htslib and also autoconfigures before compilation, but it does no work on my computer, not sure why

  KamilSJaron

  committed
  030282f

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Commits on Feb 12, 2020

• Added depth ratio column to window output file

  RomainFeron

  committed
  816b0c4

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Commits on Feb 10, 2020

• Added contig lengths to snp and fst output files

  RomainFeron

  committed
  f63a57a

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Commits on Feb 9, 2020

• Fixed contig length output, updated readme

  RomainFeron

  committed
  b660b49

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• Added contig length to window output file

  RomainFeron

  committed
  76d56b5

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• Implemented output file option in psass pileup

  RomainFeron

  committed
  95a66d7

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• Minr readme update

  RomainFeron

  committed
  43d4e57

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• Fixed typo in argument parser for kpool

  RomainFeron

  committed
  3fad245

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• Added short options to CLI arguments

  RomainFeron

  committed
  18e4e55

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• Updated README and added small fixes to parameters / output file

  RomainFeron

  committed
  82e9cd3

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Commits on Feb 7, 2020

• Updated gitignore for htslib

  RomainFeron

  committed
  d87989d

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• Fixed gitignore not including test folder in htslib

  RomainFeron

  committed
  dcb68da

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• Ported kpool code to extract pool-specific kmers from a merged kmer table

  RomainFeron

  committed
  4f71fa8

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• Fixed bug opening first kmer table for both pools

  RomainFeron

  committed
  2d4dd52

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• Ported kpool code to merge two kmer counts tables

  RomainFeron

  committed
  0c3629d

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• Updated file structure and makefile to prepare for multiple targets

  RomainFeron

  committed
  6dab011

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• Build index for BAM/CRAM files when missing; fixed building index for reference bug

  RomainFeron

  committed
  39420f3

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