ukhsa-collaboration/PHEnix

Issues

• How does PHEnix handle plasmids?

  #46 opened 4 years ago by flashton2003
  2

• Is public release mirroring PHE version?

  #45 opened 4 years ago by flashton2003
  2

• SNP filtering really slow

  #44 opened 6 years ago by BertBog
  11

• Strict requirements for old version of numpy?

  #43 opened 6 years ago by russellsmithies
  4

• Relax the versions of dependencies?

  #41 opened 6 years ago by tseemann
  4

• Change pip to pip2 in README

  #42 opened 6 years ago by tseemann
  1

• Add to README `pip install` directly from `github`

  #31 opened 6 years ago by andersgs
  1

• Can PHEnix output consensus genome?

  #35 opened 6 years ago by flashton2003
  5

• Crash when calculating memory before samtools sort

  #36 opened 6 years ago by timdallman
  2

• A small typo in README

  #39 opened 7 years ago by thanhleviet
  1

• Tests directory contains broken symlinks

  #38 opened 7 years ago by pvanheus
  1

• Issues in setup.py

  #37 opened 7 years ago by mbargull
  4

• Don't use file handles to store data

  #21 opened 7 years ago by alexjironkin
  3

• More accurate progress indicator

  #28 opened 7 years ago by antunderwood
  1

• Could requirement of biopython==1.65 be relaxed to biopython>=1.65?

  #32 opened 7 years ago by andersgs
  1

• Broken link in docs

  #34 opened 7 years ago by tseemann
  0

• Issue Running PHEnix on CentOS7 build

  #30 opened 8 years ago by Andybacon76
  4

• Why does it say "PHEnix-N-A" without version ?

  #24 opened 8 years ago by tseemann
  0

• phenix.py is not installed into bin/

  #23 opened 8 years ago by tseemann
  0

• Add, 'add to pythonpath' to instructions

  #22 opened 8 years ago by flashton2003
  5

• Warning: FastBinaryTree not available - how to fix?

  #25 opened 8 years ago by tseemann
  5

• why is parse vcf so slow?

  #27 opened 8 years ago by flashton2003
  4

• Add module for Freebayes variant caller

  #7 opened 8 years ago by tseemann
  0

• Add module for Pilon variant caller

  #8 opened 8 years ago by tseemann
  1

• LowQual on REF base.

  #9 opened 8 years ago by alexjironkin
  8

• What base to use in FASTA files

  #10 opened 8 years ago by alexjironkin
  1

• Summary after filtering VCF

  #20 opened 8 years ago by alexjironkin
  0

• Options -m and -v not recognised

  #19 opened 8 years ago by gkapatai
  2

• shebang and executable on run_snp_pipeline.py

  #17 opened 8 years ago by antunderwood
  3

• Cleanup?

  #18 opened 8 years ago by antunderwood
  0

• Variable name breaks vcf2fasta

  #16 opened 8 years ago by antunderwood
  1

• N in VCF for mpileup

  #13 opened 8 years ago by alexjironkin
  1

• Better memory usage for run_snp_pipeline.

  #12 opened 8 years ago by alexjironkin
  6

• Documentation update required

  #11 opened 8 years ago by antunderwood
  0

• Replace 'blurb' with actual links in README.md

  #5 opened 8 years ago by tseemann
  3

• prepare_reference.py doesn't do anything?

  #4 opened 8 years ago by tseemann
  2

• Add validate() method.

  #6 opened 8 years ago by alexjironkin
  1

• Confusion over name - PHEnix or Phoenix ?

  #2 opened 8 years ago by tseemann
  9

• No installation instructions

  #3 opened 8 years ago by tseemann
  2

• "Build status" badge in README - image is broken

  #1 opened 8 years ago by tseemann
  3