Uploaded variation name #118
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…to be finished as they need to use the synonym file
* postreleasefix/91: version update suppress recursion warnings clogging up web logs on bad user input dont dump LRG slices for refseq cache remove break point
* postreleasefix/91: dump_vep_otherfeatures should wait for all the core create_dump_jobs to be finished as they need to use the synonym file
* postreleasefix/91: fix for missing info fields in converted variation cache BAM_EDIT field missing from VCF output
* postreleasefix/91: fix when name is 0 in BED
* postreleasefix/91: add --vcf_info_field to help message add missing cell_type flag Refine filter_vep handling of VCF
Transfer functionality from miRNA.pm plugin to main VEP code
* postreleasefix/91: add hardcoded frequency test variants fix var cache info error cat into sort prevents running out of memory subversion update check defined before sedding gene_symbol should be exempt from numberification in JSON output remove any whitespace crud from input freeze installed Bio-DB-HTS version, move other installed versions to top for clarity
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To backward compatibility and to be equal with documentation is necessary to make a correction in 'modules/Bio/EnsEMBL/VEP/OutputFactory.pm' line 783.
-Uploaded_variation => $vf->variation_name,
+Uploaded_variation => $vf->variation_name ne '.' ? $vf->variation_name : ($vf->{original_chr} || $vf->{chr}).''.$vf->{start}.''.($vf->{allele_string} || $vf->{class_SO_term}),
From your help:
"""
The default output format ("VEP" format when downloading from the web interface) is a 14 column tab-delimited file. Empty values are denoted by '-'. The output columns are:
'Uploaded variation - as chromosome_start_alleles'
"""