This project is mirrored from https://:*****@github.com/Ensembl/ensembl-io.git.
Pull mirroring updated .
- May 08, 2018
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Alessandro Vullo authored
[ENSCORESW-2708] added pull request template
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- Apr 19, 2018
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Brandon Walts authored
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Brandon Walts authored
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- Apr 03, 2018
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Alessandro Vullo authored
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Alessandro Vullo authored
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Alessandro Vullo authored
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Alessandro Vullo authored
[ENSCORESW-2690]. Close only if we've really got an iterator, can get an empty hash ref under special cases.
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- Feb 19, 2018
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Kieron Taylor authored
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- Jan 15, 2018
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Thomas Maurel authored
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- Nov 13, 2017
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William McLaren authored
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William McLaren authored
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William McLaren authored
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- Oct 24, 2017
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Alessandro Vullo authored
Travis switch to Trusty which does not support mysql-5.5. Explicitly start whatever mysql service is available.
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- Oct 04, 2017
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Anne Lyle authored
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- Sep 13, 2017
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Matthew Laird authored
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- Aug 21, 2017
- Aug 14, 2017
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William McLaren authored
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- Jul 19, 2017
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Anne Lyle authored
Rework on how Bio::DB::HTS is used in HTSAdaptor
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Harpreet Riat authored
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Anne Lyle authored
Add VCF4 format for validation
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- Jul 14, 2017
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Zhicheng Liu authored
as spaces can appear within a field which means it is not safe to use space as delimiter. Now I found a way to make tab delimiter work for me so the space is no longer needed anyway.
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- Jul 13, 2017
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Zhicheng Liu authored
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Zhicheng Liu authored
Previoiusly because of the lack of VCF4 format definition, the user upload of VCF type data (stored in text) could not be validated. This change is intended to add this missing information so that those VCF records could be validated and parsed. Also add space as a valid delimiter in addition to tab. I know this is violating the VCF4.x spece. But I could not get tab delimited VCF record to work. I don't know why. Related to ENSEMBL-5050.
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Anne Lyle authored
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Anne Lyle authored
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- Jun 28, 2017
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Zhicheng Liu authored
based on Mag's review comments at this pull request: https://github.com/Ensembl/ensembl-io/pull/55
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Zhicheng Liu authored
The Bio::DB::HTS object and other relatedHTS objects will be created only once within a single HTSAdaptor. They will have only one copy and be stored in $self->{_cache}->{_htsobj_handle}. Every use of HTS objects should through this copy. Also remove "close" calls to the HTS objects as these objects will handle their resources properly when exiting. The DESTROY methods to these objects has been added in https://github.com/Ensembl/Bio-DB-HTS/pull/50 which will release the resources where needed. This will provide a uniform interface to HTS objects, making it more consistent. It prevents from creating multiple objects for the same file and hence more resouces efficient too. Also rename some variables to make them consistent throughout. Related to ENSEMBL-5035.
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- Jun 27, 2017
- Jun 13, 2017
- Jun 12, 2017
- May 19, 2017
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Anne Lyle authored
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- Mar 14, 2017
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William McLaren authored
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William McLaren authored
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