ensembl-io merge requestshttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests2017-06-30T08:15:44Zhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/54Experimental/unified design2017-06-30T08:15:44ZMarek SzubaExperimental/unified design*Created by: avullo*
This is introducing RDF writers for features (non ensembl) and corresponding xrefs.
Includes a minor change on the way taxonomy data is described.*Created by: avullo*
This is introducing RDF writers for features (non ensembl) and corresponding xrefs.
Includes a minor change on the way taxonomy data is described.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/41Update URL.pm2016-05-24T14:05:35ZMarek SzubaUpdate URL.pm*Created by: ens-ma7*
added method to download file to local file system
*Created by: ens-ma7*
added method to download file to local file system
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/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.
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/38exclude samples with uncalled genotypes2016-05-06T14:32:20ZMarek Szubaexclude samples with uncalled genotypes*Created by: at7*
Ignore samples with uncalled genotypes. This came up because of a display error of genotype counts. This is also a post-release for ensembl genomes. (ENSVAR-326)
*Created by: at7*
Ignore samples with uncalled genotypes. This came up because of a display error of genotype counts. This is also a post-release for ensembl genomes. (ENSVAR-326)
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/47correct tabix header function called in PairwiseAdaptor.pm2018-12-17T16:17:46ZMarek Szubacorrect tabix header function called in PairwiseAdaptor.pm*Created by: rishidev*
Call the correct function from Bio::DB::HTS Tabix
*Created by: rishidev*
Call the correct function from Bio::DB::HTS Tabix
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/42Update fetch_file in URL.pm2016-05-25T10:16:38ZMarek SzubaUpdate fetch_file in URL.pm*Created by: ens-ma7*
return downloaded file destination on local file system
*Created by: ens-ma7*
return downloaded file destination on local file system
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/43call DESTROY to close tabix file2016-05-31T09:36:16ZMarek Szubacall DESTROY to close tabix file*Created by: rishidev*
Changes in Bio::DB::HTS::Tabix means the DESTROY function should be called instead of the close to pass Tabix tests.
*Created by: rishidev*
Changes in Bio::DB::HTS::Tabix means the DESTROY function should be called instead of the close to pass Tabix tests.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/40Munge for Chr in HTSAdaptor as was for BAM Adaptor2016-05-09T14:52:36ZMarek SzubaMunge for Chr in HTSAdaptor as was for BAM Adaptor*Created by: rishidev*
*Created by: rishidev*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/32Existing TABIX functionality via Bio::DB::HTS2016-03-15T15:09:53ZMarek SzubaExisting TABIX functionality via Bio::DB::HTS*Created by: rishidev*
This upgrades ensembl-io to use tabix functionality from Bio::DB::HTS (https://github.com/Ensembl/Bio-HTS) and HTSlib to improve performance rather than calling the command line executable. It passes the tabix rel...*Created by: rishidev*
This upgrades ensembl-io to use tabix functionality from Bio::DB::HTS (https://github.com/Ensembl/Bio-HTS) and HTSlib to improve performance rather than calling the command line executable. It passes the tabix related t tests but I think these fail for other reasons.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/29Alter genotype field return type2016-02-24T13:52:35ZMarek SzubaAlter genotype field return type*Created by: willmclaren*
get_raw_samples_info() was returning a ":"-delimited string where
the first element was the sample name. This broke downstream methods
when the sample name contained ":", so the method has been changed
to retur...*Created by: willmclaren*
get_raw_samples_info() was returning a ":"-delimited string where
the first element was the sample name. This broke downstream methods
when the sample name contained ":", so the method has been changed
to return a listref instead.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/30Alter genotype field return type2016-02-23T12:54:57ZMarek SzubaAlter genotype field return type*Created by: willmclaren*
get_raw_samples_info() was returning a ":"-delimited string where
the first element was the sample name. This broke downstream methods
when the sample name contained ":", so the method has been changed
to retur...*Created by: willmclaren*
get_raw_samples_info() was returning a ":"-delimited string where
the first element was the sample name. This broke downstream methods
when the sample name contained ":", so the method has been changed
to return a listref instead.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/23Existing patches to make bigfile fail softly.2015-12-03T12:53:02ZMarek SzubaExisting patches to make bigfile fail softly.*Created by: ens-ds23*
This is the existing C code patches for local modifications to the UCSC and CPAN bigfile libraries, to make them not fail so horribly when a track is unavailable. They are already live, but are just hanging around...*Created by: ens-ds23*
This is the existing C code patches for local modifications to the UCSC and CPAN bigfile libraries, to make them not fail so horribly when a track is unavailable. They are already live, but are just hanging around in my home directory. After talking with Anne, we decided that this is the best place for them. It's ok for them just to go onto master as they're only needed at compile-time.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/26add is_polymorphic method to aid LD genotype retrieval2016-01-15T11:22:05ZMarek Szubaadd is_polymorphic method to aid LD genotype retrieval*Created by: willmclaren*
*Created by: willmclaren*
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/22code now also checks for Chr2016-05-06T12:34:56ZMarek Szubacode now also checks for Chr*Created by: rishidev*
Added a check for cases where Chr is used in the BAM file in BAMAdaptor
*Created by: rishidev*
Added a check for cases where Chr is used in the BAM file in BAMAdaptor
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/25Feature/htslib adds HTSAdaptor.pm2016-01-04T10:05:13ZMarek SzubaFeature/htslib adds HTSAdaptor.pm*Created by: rishidev*
HTSAdaptor uses HTSlib to read values in BAM and CRAM files. The changes have been tested with ensembl-webcode for producing reads and coverage displays for BAM and CRAM files.
*Created by: rishidev*
HTSAdaptor uses HTSlib to read values in BAM and CRAM files. The changes have been tested with ensembl-webcode for producing reads and coverage displays for BAM and CRAM files.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/28Meaningful help on HTTP::Tiny errors.2016-02-18T09:49:14ZMarek SzubaMeaningful help on HTTP::Tiny errors.*Created by: ens-ds23*
HTTP::Tiny uses status code 599 for internal errors and puts a
description in the /body/, not the status line, which uselessly says
"Internal Exception". When reporting errors for status 599, use
content, not stat...*Created by: ens-ds23*
HTTP::Tiny uses status code 599 for internal errors and puts a
description in the /body/, not the status line, which uselessly says
"Internal Exception". When reporting errors for status 599, use
content, not status line to report back up the chain.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/21- Fixed bug in Fasta parser, where if the sequence wasn't accessed wh…2018-12-17T16:17:55ZMarek Szuba- Fixed bug in Fasta parser, where if the sequence wasn't accessed wh…*Created by: lairdm*
…en cycling through records the pointer didn't advance correctly (one too many records was reported existing)
- Added support for Fasta embedded in GFF3 files via an embedded Fasta parser when the ##FASTA tag is rea...*Created by: lairdm*
…en cycling through records the pointer didn't advance correctly (one too many records was reported existing)
- Added support for Fasta embedded in GFF3 files via an embedded Fasta parser when the ##FASTA tag is reached
- Made the return from read_block() explicit