phe-bioinformatics/PHEnix issues and pull requests

#46 - How does PHEnix handle plasmids?

Issue - State: open - Opened by flashton2003 over 3 years ago - 2 comments

#45 - Is public release mirroring PHE version?

Issue - State: closed - Opened by flashton2003 about 4 years ago - 2 comments

#44 - SNP filtering really slow

Issue - State: closed - Opened by BertBog almost 6 years ago - 11 comments

#43 - Strict requirements for old version of numpy?

Issue - State: closed - Opened by russellsmithies almost 6 years ago - 4 comments

#42 - Change pip to pip2 in README

Issue - State: closed - Opened by tseemann about 6 years ago - 1 comment

#41 - Relax the versions of dependencies?

Issue - State: closed - Opened by tseemann about 6 years ago - 4 comments

#40 - Fix typo in setup.py causing it to silently fail installation

Pull Request - State: closed - Opened by andersgs over 6 years ago - 2 comments

#39 - A small typo in README

Issue - State: closed - Opened by thanhleviet over 6 years ago - 1 comment

#38 - Tests directory contains broken symlinks

Issue - State: open - Opened by pvanheus over 6 years ago - 1 comment

#37 - Issues in setup.py

Issue - State: open - Opened by mbargull over 6 years ago - 4 comments

#36 - Crash when calculating memory before samtools sort

Issue - State: closed - Opened by timdallman over 6 years ago - 2 comments

#35 - Can PHEnix output consensus genome?

Issue - State: closed - Opened by flashton2003 over 6 years ago - 5 comments

#34 - Broken link in docs

Issue - State: open - Opened by tseemann about 7 years ago

#33 - correct max vcf size finding

Pull Request - State: closed - Opened by antunderwood about 7 years ago

#32 - Could requirement of biopython==1.65 be relaxed to biopython>=1.65?

Issue - State: closed - Opened by andersgs over 7 years ago - 1 comment

#31 - Add to README `pip install` directly from `github`

Issue - State: closed - Opened by andersgs over 7 years ago - 1 comment

#30 - Issue Running PHEnix on CentOS7 build

Issue - State: closed - Opened by Andybacon76 over 7 years ago - 4 comments

#29 - rather than guestimate from first vcf choose largest vcf so as not to disappoint

Pull Request - State: open - Opened by antunderwood over 7 years ago

#28 - More accurate progress indicator

Issue - State: closed - Opened by antunderwood over 7 years ago - 1 comment
Labels: enhancement

#27 - why is parse vcf so slow?

Issue - State: closed - Opened by flashton2003 almost 8 years ago - 4 comments
Labels: question

#26 - added a few things to readme

Pull Request - State: open - Opened by flashton2003 almost 8 years ago - 1 comment

#25 - Warning: FastBinaryTree not available - how to fix?

Issue - State: closed - Opened by tseemann almost 8 years ago - 5 comments
Labels: question

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

Issue - State: closed - Opened by tseemann almost 8 years ago
Labels: bug

#23 - phenix.py is not installed into bin/

Issue - State: closed - Opened by tseemann almost 8 years ago
Labels: bug, enhancement

#22 - Add, 'add to pythonpath' to instructions

Issue - State: closed - Opened by flashton2003 almost 8 years ago - 5 comments
Labels: duplicate, wontfix

#21 - Don't use file handles to store data

Issue - State: closed - Opened by alexjironkin almost 8 years ago - 3 comments
Labels: enhancement

#20 - Summary after filtering VCF

Issue - State: open - Opened by alexjironkin almost 8 years ago
Labels: enhancement

#19 - Options -m and -v not recognised

Issue - State: closed - Opened by gkapatai almost 8 years ago - 2 comments

#18 - Cleanup?

Issue - State: closed - Opened by antunderwood about 8 years ago

#17 - shebang and executable on run_snp_pipeline.py

Issue - State: closed - Opened by antunderwood about 8 years ago - 3 comments

#16 - Variable name breaks vcf2fasta

Issue - State: closed - Opened by antunderwood about 8 years ago - 1 comment

#15 - Memory optimisations

Pull Request - State: closed - Opened by alexjironkin about 8 years ago

#14 - Memory optimisations

Pull Request - State: closed - Opened by alexjironkin about 8 years ago

#13 - N in VCF for mpileup

Issue - State: closed - Opened by alexjironkin about 8 years ago - 1 comment

#12 - Better memory usage for run_snp_pipeline.

Issue - State: closed - Opened by alexjironkin about 8 years ago - 6 comments

#11 - Documentation update required

Issue - State: closed - Opened by antunderwood about 8 years ago

#10 - What base to use in FASTA files

Issue - State: open - Opened by alexjironkin about 8 years ago - 1 comment
Labels: enhancement, question

#9 - LowQual on REF base.

Issue - State: open - Opened by alexjironkin about 8 years ago - 8 comments
Labels: question

#8 - Add module for Pilon variant caller

Issue - State: open - Opened by tseemann about 8 years ago - 1 comment
Labels: enhancement

#7 - Add module for Freebayes variant caller

Issue - State: open - Opened by tseemann about 8 years ago
Labels: enhancement

#6 - Add validate() method.

Issue - State: closed - Opened by alexjironkin about 8 years ago - 1 comment
Labels: enhancement

#5 - Replace 'blurb' with actual links in README.md

Issue - State: closed - Opened by tseemann about 8 years ago - 3 comments

#4 - prepare_reference.py doesn't do anything?

Issue - State: closed - Opened by tseemann about 8 years ago - 2 comments
Labels: enhancement

#3 - No installation instructions

Issue - State: closed - Opened by tseemann about 8 years ago - 2 comments

#2 - Confusion over name - PHEnix or Phoenix ?

Issue - State: closed - Opened by tseemann about 8 years ago - 9 comments
Labels: enhancement

#1 - "Build status" badge in README - image is broken

Issue - State: closed - Opened by tseemann about 8 years ago - 3 comments

GitHub / phe-bioinformatics/PHEnix issues and pull requests