ensembl-io merge requestshttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests2020-01-22T12:42:13Zhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/83ancestral_allele update2020-01-22T12:42:13ZMarek Szubaancestral_allele update*Created by: tgrego*
Variation `Bio::EnsEMBL::Variation::Variation::ancestral_allele` method has been deprecated and replaced with `Bio::EnsEMBL::Variation::VariationFeature::ancestral_allele`.
`Bio::EnsEMBL::IO::Translator::SampleGe...*Created by: tgrego*
Variation `Bio::EnsEMBL::Variation::Variation::ancestral_allele` method has been deprecated and replaced with `Bio::EnsEMBL::Variation::VariationFeature::ancestral_allele`.
`Bio::EnsEMBL::IO::Translator::SampleGenotypeFeature` uses the deprecated method and is now failing, so an update is required.
This fixes the issue by patching the test DBs and the test data object, and updated the deprecated method to the new one.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/73Yearly copyright update2020-01-22T12:43:12ZMarek SzubaYearly copyright update*Created by: tgrego*
2019 yearly copyright update*Created by: tgrego*
2019 yearly copyright updatehttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/79ensembl Utils::IO into ensembl-io2020-01-22T12:42:17ZMarek Szubaensembl Utils::IO into ensembl-io*Created by: tgrego*
`Bio::EnsEMBL::Utils::IO::*` lives in the core repo at the moment.
This code predates the ensembl-io code, but it sure is IO related and should probably be located there.
This pull request moves that code into the...*Created by: tgrego*
`Bio::EnsEMBL::Utils::IO::*` lives in the core repo at the moment.
This code predates the ensembl-io code, but it sure is IO related and should probably be located there.
This pull request moves that code into the ensembl-io repo, keeping the same namespace. Thus code that uses it will not need any changes except that ensembl-io will now be a dependency.
This code was developed with the intention if being used internally by the production team, so it should be possible to let them know before branching of release/97.
Four filetypes were identified as being dealt with by both ensembl-io and utils-io: GTF, GFF, FASTA and BED.
Extra tests were added to check that the output of files produced by utils/io and ensembl-io are similar where they should be (t/utils_io/harmony.t). This is completed for the GTF and GFF formats (although only gene objects are tested at the moment... it's also easy to extend the test cases).
BED format seems however to be written in different formats by the 2 systems, thus there is only a stud for the test and more investigation required.
FASTA seems to be feature incomplete in ensembl-io (parser only), thus there is only a stud for the test and more investigation required (implementation of a FASTA writer needed?).
Utils/IO in the core repo can then possibly be deleted if this is working fine. I think the 4 release deprecation notice does not apply here as this is not really a deprecation but a move...
Namespace is the same, code is the same, all should be fine with the dependencies updated.
Coordinated with this https://github.com/Ensembl/ensembl/pull/368 has been submitted.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/3fix misuse of get_alternatives in get_start2014-10-24T15:13:31ZMarek Szubafix misuse of get_alternatives in get_start*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/37exclude samples with uncalled genotypes2016-05-05T09:05:52ZMarek Szubaexclude samples with uncalled genotypes*Created by: at7*
Ignore samples with uncalled genotypes. This came up because of a display error of genotype counts.
*Created by: at7*
Ignore samples with uncalled genotypes. This came up because of a display error of genotype counts.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/36Bio::DB::HTS requirements added to README2016-04-28T09:54:23ZMarek SzubaBio::DB::HTS requirements added to README*Created by: rishidev*
Letting the user know Bio::DB::HTS is required in certain situations.
*Created by: rishidev*
Letting the user know Bio::DB::HTS is required in certain situations.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/80Reinstate line deleted by accident2019-02-22T13:27:14ZMarek SzubaReinstate line deleted by accident*Created by: ens-ap5*
As per discussion with Mark & Tiago on 21/02/19*Created by: ens-ap5*
As per discussion with Mark & Tiago on 21/02/19https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/88Travis: explicitly use Ubuntu Trusty for builds2019-06-25T12:08:02ZMarek SzubaTravis: explicitly use Ubuntu Trusty for builds*Created by: mkszuba*
## Use case
Make sure we are not affected by the ongoing change of the default Travis build environment from Ubuntu Trusty to Ubuntu Xenial, for which we are not ready yet, by explicitly requesting the former.
...*Created by: mkszuba*
## Use case
Make sure we are not affected by the ongoing change of the default Travis build environment from Ubuntu Trusty to Ubuntu Xenial, for which we are not ready yet, by explicitly requesting the former.
## Description
It has turned out that in spite of what the Travis documentation says, perl-5.14 is *not* available under the Xenial environment on Travis. We still require compatibility with that Perl version so it is necessary for us to make sure we continue to use Trusty even after the default Travis environment has been changed to Xenial, a change that is now in progress following the end of life of Ubuntu Trusty (see https://blog.travis-ci.com/2019-04-15-xenial-default-build-environment).
## Possible Drawbacks
Ubuntu Trusty has already reached end of life.
## Testing
_Have you added/modified unit tests to test the changes?_
No, changes affect Travis only.
_If so, do the tests pass/fail?_
N/A
_Have you run the entire test suite and no regression was detected?_
No, changes affect Travis only.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/51Improvements to munge_chr_id subroutine in HTSAdaptor2018-12-17T16:17:42ZMarek SzubaImprovements to munge_chr_id subroutine in HTSAdaptor*Created by: rishidev*
Various improvements to the munge_chr_id subroutine in HTSAdaptor, which were causing a crash on web when zooming in to view BAM/CRAM files.
1. changed the call to get a file handle directly from Bio::DB::HTS dir...*Created by: rishidev*
Various improvements to the munge_chr_id subroutine in HTSAdaptor, which were causing a crash on web when zooming in to view BAM/CRAM files.
1. changed the call to get a file handle directly from Bio::DB::HTS directly instead of re-using the call to the HTSAdaptors own htsfile open
2. We don't need the 1:1 in the region specifier with HTSlib
3. calls to $htsfile->close() ; before returning a value
4. removed unused ret_id variable
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/8Non-extended summary retrieval for BigWigs.2015-04-23T14:08:06ZMarek SzubaNon-extended summary retrieval for BigWigs.*Created by: ens-ds23*
Saves us having to do the computation ourselves.
*Created by: ens-ds23*
Saves us having to do the computation ourselves.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/84README: Use the same badge syntax as for 'ensembl'2019-06-17T14:45:50ZMarek SzubaREADME: Use the same badge syntax as for 'ensembl'*Created by: mkszuba*
i.e. both Travis and Coveralls, explicitly specify the branch*Created by: mkszuba*
i.e. both Travis and Coveralls, explicitly specify the branchhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/6fix when individual_ids not defined2015-03-30T13:09:14ZMarek Szubafix when individual_ids not defined*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/48First try for a VCF4 writer2017-01-09T09:31:34ZMarek SzubaFirst try for a VCF4 writer*Created by: ens-lgil*
*Created by: ens-lgil*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/49EnsEMBL::Web::Tree changed2018-12-17T16:17:44ZMarek SzubaEnsEMBL::Web::Tree changed*Created by: ens-hsr*
*Created by: ens-hsr*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/11fix for slightly clumsy passing of args to synonym methods2015-06-02T09:41:19ZMarek Szubafix for slightly clumsy passing of args to synonym methods*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/2Add some new features and fixes for the VCF backend code in the Variation API2014-10-08T10:06:45ZMarek SzubaAdd some new features and fixes for the VCF backend code in the Variation API*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/55Rework on how Bio::DB::HTS is used in HTSAdaptor2017-07-19T10:07:55ZMarek SzubaRework on how Bio::DB::HTS is used in HTSAdaptor*Created by: Zhicheng-Liu*
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 ob...*Created by: Zhicheng-Liu*
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.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/63Fix of hard coded test data file paths in tests2018-08-13T10:14:35ZMarek SzubaFix of hard coded test data file paths in tests*Created by: tgrego*
## Description
Tests used an absolute path for the test files, so if test where run from a different location other than the root of the repo it would fail to find the files.
This changes the path to a relativ...*Created by: tgrego*
## Description
Tests used an absolute path for the test files, so if test where run from a different location other than the root of the repo it would fail to find the files.
This changes the path to a relative path, so that it always finds the test files.
## Use case
Tests are sometimes run from locations other than the root of the repo, and it would fail to find the test files.
## Benefits
Path for test files is now always correct.
## Possible Drawbacks
none I can think of.
## Testing
_Have you added/modified unit tests to test the changes?_
yes
_If so, do the tests pass/fail?_
pass
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/58[ENSCORESW-2708] added pull request template2018-12-17T16:17:32ZMarek Szuba[ENSCORESW-2708] added pull request template*Created by: ens-bwalts*
*Created by: ens-bwalts*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/35htsfile close function added2016-04-15T13:48:36ZMarek Szubahtsfile close function added*Created by: rishidev*
Function to close the file handle after it is no longer needed.
*Created by: rishidev*
Function to close the file handle after it is no longer needed.