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https://github.com/mendelics/vcf

Variant Call Format parser library for Go
https://github.com/mendelics/vcf

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Variant Call Format parser library for Go

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vcf

===



`vcf` is a `golang` package that parses data from an `io.Reader` adhering to the [Variant Call Format v4.2 Specification](https://samtools.github.io/hts-specs/VCFv4.2.pdf).



Data is read asynchronously and returned through two channels, one with correctly parsed variants and one with unknown variants whose parsing failed. Proper initialization and buffering of these channels is a responsibility of the client.



This package is still work in progress, subject to change at any time without notice. Releases will follow [Semantic Versioning 2.0.0](http://semver.org/spec/v2.0.0.html). Major is still in `v0` to reflect the early stage development this package is in.



### INFO



Currently, parsing can handle Samples, optional fields such as ID, Quality and Filter, as well as the INFO field. INFO is exposed in two ways:



* As a `map[string]interface{}` exposing all fields found on the INFO for each variant, without any treatment. Key-value pairs are added to this map. In the case of keys such as `DB` which don't have a value, the value used is a `true` boolean.

* As a series of sub-fields listed on section `1.4.1-8` of the [VCF 4.2 spec](https://samtools.github.io/hts-specs/VCFv4.2.pdf). These sub-fields are provided in a best effort manner. Failure to parse one of these sub-fields will only cause its corresponding pointer to be `nil`, not generating an error. The raw data can always be found on the map.



### Genotype fields



Genotype fields (section `1.4.2` on the [spec](https://samtools.github.io/hts-specs/VCFv4.2.pdf)) do not have the same kind of treatment yet. They are separated by sample, but the only form represented is a raw map. Easy access to sub-fields is intended in the future.



### Structural variants



Structural variants have not been addressed as of version [`0.1.0`](https://github.com/mendelics/vcf/releases/tag/0.1.0).



### License



This software uses the [BSD 3-Clause License](http://opensource.org/licenses/BSD-3-Clause).



---



Copyright (c) 2015, Mendelics Análise Genômica S.A.

All rights reserved.



Redistribution and use in source and binary forms, with or without

modification, are permitted provided that the following conditions are met:



* Redistributions of source code must retain the above copyright notice, this

  list of conditions and the following disclaimer.



* Redistributions in binary form must reproduce the above copyright notice,

  this list of conditions and the following disclaimer in the documentation

  and/or other materials provided with the distribution.



* Neither the name of the copyright holder nor the names of its contributors

  may be used to endorse or promote products derived from this software

  without specific prior written permission.



THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"

AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE

FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL

DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR

SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER

CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,

OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.