ensembl-io merge requestshttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests2016-05-24T14:05:35Zhttps://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/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/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/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/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/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/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/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/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/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/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/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/31'defined' will return 1 if compression is provided2018-12-17T16:17:52ZMarek Szuba'defined' will return 1 if compression is provided*Created by: ens-hsr*
release/84 and master are already diverged, so please add this to master too.
*Created by: ens-hsr*
release/84 and master are already diverged, so please add this to master too.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/ensembl-io/-/merge_requests/31'defined' will return 1 if compression is provided2018-12-17T16:17:52ZMarek Szuba'defined' will return 1 if compression is provided*Created by: ens-hsr*
release/84 and master are already diverged, so please add this to master too.
*Created by: ens-hsr*
release/84 and master are already diverged, so please add this to master too.
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/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/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/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.