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    Zev Kronenberg
    @zeeev
    @ekg If you create an organization and transfer vcflib's ownership to it i can then use my Travis-CI. Otherwise you will need to to do it.
    Zev Kronenberg
    @zeeev
    @ekg we're getting out of sync between vcflib/vcflib and ekg/vcflib
    Erik Garrison
    @ekg
    Is there a way to set up a redirect?
    Zev Kronenberg
    @zeeev
    it's tricky because ekg/vcflib is so well known
    it might just be smarter to stick with ekg/vcflib?
    Zev Kronenberg
    @zeeev
    @ekg We've got a massive memory leak via tabixpp
    Seb Horsewell
    @sebkajeka
    Also make it easier to build cross platform :
    Zev Kronenberg
    @zeeev
    @sebkajeka ?
    Seb Horsewell
    @sebkajeka
    I want to build a .dll for windows
    Any specific route I should be taking?
    Zev Kronenberg
    @zeeev
    @sebkajeka Sorry it's been so long since i've been on a windows machine, does windows have lib?
    "zlib"
    Seb Horsewell
    @sebkajeka
    That's the issue I've been having yeah
    The tool i've been building runs on everything (Linux, OSX, Windows)
    Zev Kronenberg
    @zeeev
    @sebkajeka where are you at in the process
    Seb Horsewell
    @sebkajeka
    Well was trying to build with make but there's a lot of Unix specific stuff in there
    So I think I need to rebuild the project in VisualStudio and make a projec
    Although I probably can't complete it in the next 30 minutes so I'll have to continue it on monday :)
    Zev Kronenberg
    @zeeev
    @sebkajeka okay
    Seb Horsewell
    @sebkajeka
    @zeeev I'll let you know if/when I get one setup. See you next week!
    Erik Garrison
    @ekg
    @zeeev oh man. How did you detect the leak?
    Zev Kronenberg
    @zeeev
    @ekg noticed that memory was climbing crazy with vcflib/vcfuniq
    @brentp and I found it
    you're not freeing kstring_t
    there is a PR
    Zev Kronenberg
    @zeeev
    @ekg ekg/tabixpp#11
    Zev Kronenberg
    @zeeev
    @ekg let me know when you get around to pulling that change so we can update the submodule pointer
    Erik Garrison
    @ekg
    I should move it to the vcflib group
    Zev Kronenberg
    @zeeev
    @ekg next time you get five minutes let's talk
    Erik Garrison
    @ekg
    @zeeev up?
    i merged in the memory leak
    fix :)
    Zev Kronenberg
    @zeeev
    @ekg thanks man
    do you know how to update the submodule in vcflib?
    Erik Garrison
    @ekg
    @zeeev yeah we just need to go into the places where tabixpp is used and ensure they're updated (e.g. git pull origin master) then commit
    it may be embedded in another submodule
    Zev Kronenberg
    @zeeev
    @ekg how do you feel about the following 4.2 spec bit: If any of the fields is missing, it is replaced with the missing value. For example if the FORMAT is GT:GQ:DP:HQ then 0 | 0 : . : 23 : 23, 34 indicates that GQ is missing. Trailing fields can be dropped (with the exception of the GT field, which should always be present if specified in the FORMAT field).
    Erik Garrison
    @ekg
    @zeeev that all makes sense to me. Whatever is needed to maintain compatibility!
    Zev Kronenberg
    @zeeev
    @ekg welp, looks like vcflib is stripping genotypes with fewer fields
    than listed
    Zev Kronenberg
    @zeeev
    i'll work on making the changes neeeded
    Seb Horsewell
    @sebkajeka
    Todays task: Port vcflib to visual studio
    Erik Garrison
    @ekg
    I think it could work. What will you do with it from VS?
    Seb Horsewell
    @sebkajeka
    I want to include some vcf capabilities in a cross-platform tool I'm developing, unfortunately I run primarily Windows and so as a starting point would like to get vcflib building here first
    At the moment I've run into an issue with getopt.h as it doesn't exist on windows. I'm attempting to shim the unix dependant code for windows
    Erik Garrison
    @ekg
    OK that's interesting. Is there no replacement library on windows? Like has someone ported getopt to vs?
    Seb Horsewell
    @sebkajeka
    It looks like their's a few partial implementations but I don't know what is being used within getopt.h yet so I'm just going to try a few
    petersam23
    @petersam23
    Hey. Would anyone mind helping me with a pretty basic question?
    Erik Garrison
    @ekg
    This chat is pretty asynchronous so its best you ask @petersam23
    Taylor Paisie
    @taylorpaisie
    Does anyone know a good way to extract a codon alignment from a vcf file output from freebayes? I’m able to get a SNP fasta alignment, but I would like to extract the codons from those SNPs in a fasta format.