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ah19 wants to merge 19 commits into from
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Allow null genotype #1

ah19 wants to merge 19 commits into from

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@ah19
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@ah19 ah19 commented Mar 26, 2018

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cfriedline and others added 19 commits October 15, 2015 16:07
@cfriedline
update parser to match pyvcf
afa035e
@bunop
Reader metadata modified in order to use OrderedDict
adb98e8 
While writing VCF metadata with the Writer class, ordering could put
the vcf file format metadata after others metadata, causing warnings
while dealing with VCF and breaking analises with the last BCF tools
@bunop
Merging Chris Friedline updates
9ab1468 
e to explain why this merge is necessary,
@bunop
Fix in VCF writer
0891c7d 
The Writer class make use of csv.writer which by default uses the windows
encoding line terminator while writing files. Forced to use the standard
'\n' newline
@ah19
Bugfix: rows with multiple filters would die when printed
2cc2725
@ah19
Always split sample names on tabs to allow spaces in sample names
bb72357
@ah19
Treat - in ALT as an indel
5e7e55f
@ah19
Properly format Flag fields when writing, and write out multi filter …
343d802 
…rows properly
@ah19
Bump version
b696d55
@ah19
Merge branch 'dev'
814e0f6
@ah19
New method for adding a header, and don't die when a new field is add…
98e6a79 
…ed to INFOS
@ah19
Include version on main module
7b5dd9a
@ah19
Bump version
c12f649
@ah19
Merge branch 'dev'
3038a9b
@ah19
Add method for adding FILTER header
56ef759
@ah19
Bump version number
4b0196f
@ah19
Default to None if no GT key present, rather than raising KeyError
7165720
@ah19
Update README to include venv instructions
26e3fa2
@ah19
Bump version number
bc60be0
@ah19 ah19 closed this Mar 26, 2018
@bunop
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bunop commented Mar 26, 2018

Hi. Thank you for the contribution. I have some considerations to make. I will do them in the next days

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bunop commented Mar 27, 2018

Thank you again for this PR #1 @ah19, some few considerations:

  • When submitting a PR, don't delete branches: pull request will be closed and the only way to deal with your code is to modify an inactive PR
  • This is a Python 2 module: python2 will be updated until 2020
  • There are now better modules do deal with VCF, I suggest cyvcf2 which incorporate htslib library and I think this is the faster library to read a VCF file in python (version 2 and 3 supported)
  • In my opinion, anaconda is a better python package manager than pyenv.

Anyway, I've integrated your code in my dev branch since I've open a pull request years ago to the original project, however I think that this is no longer mantained.

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3 participants

@ah19 @bunop @cfriedline