Re: [VCFtools-spec] VCF Specs changelog, differences between version 4.1 and 4.2

[Tim P. <tim...@gm...>]

Hi Petr,

Thank you for your reply, I had not spotted the changes section in the
4.3 spec.

It turns out that the data file I am using is actually in 4.0 format.

As I have dug deeper I have found that the differences between 4.1 and
4.2 are not important for my task,
and it seems that this is likely to be true for 4.0.

It would be good to have a copy of the 4.0 spec on the site to be able
to check.

best regards
Tim


On 23 November 2015 at 22:38, Petr Danecek  wrote:
> Hi Tim,
>
> as far as I know there isn't a good summary of changes between 4.1 and
> 4.2, but there were few. A summary of changes between 4.2 and 4.3 is
> part of the 4.3 document, PDF is available here
> http://samtools.github.io/hts-specs/
>
> Unless you want to write your own VCF parser in python, you might
> consider using programs like bcftools, which allows you to manipulate
> VCF/BCF files and quickly extract all kinds of information.
> http://samtools.github.io/bcftools/bcftools.html#query
>
> Best wishes,
> Petr
>
>
> On Sun, 2015-11-22 at 23:41 +0000, Tim Pizey wrote:
>> Hi,
>>
>> I am new to this world, so I apologise in advance if these questions
>> are ignorant.
>>
>> I need to parse a file in VCFv4.2 format and have been able to find a
>> parser written in Python to parse files in VCFv4.1 format at
>> https://github.com/jamescasbon/PyVCF
>>
>> There is no change log associated with the specification files, or
>> section within the specification which gives the changes from the
>> previous version.
>>
>> I have done a diff on VCFv4.1.tex and VCFv4.2.tex, and think that I
>> can use that for my purposes but I have also done a diff between
>> VCFv4.2.tex and  VCFv4.3.tex and the changes are too numerous and
>> complex for a diff to be the right way to tell them apart.
>>
>> Could someone more familiar with the specifications and the process of
>> creating them add a changelog summarising the differences between
>> versions?
>>
>> I would also appreciate comments on what the consequences are likely
>> to be of using a 4.1 parser on a 4.2 file.
>>
>> best regards
>> Tim Pizey
>>


-- 
Tim Pizey - http://tim.pizey.uk/