jannovar download problem

Question

[curious]

I am trying to convert some HGVS to chrom:pos:ref:alt format. I was thinking to use jannovar. As per the documentation I run:

jannovar download -d hg19/refseq

which gives me this:

Options
JannovarDownloadOptions [downloadDir=data, getDataSourceFiles()=[bundle:///default_sources.ini], isReportProgress()=true, getHttpProxy()=null, getHttpsProxy()=null, getFtpProxy()=null, geneIdentifiers=[], outputFile=]
Downloading/parsing for data source "hg19/refseq"
INFO Downloading data...
INFO Downloading https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz
INFO Creating directory data/hg19/refseq
[==================================================]   100%
INFO Downloaded file ref_GRCh37.p13_top_level.gff3.gz looks like a valid gzip'ed file
INFO Downloading https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz
[==================================================]   100%
INFO Downloaded file rna.fa.gz looks like a valid gzip'ed file
INFO Downloading http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
[==================================================]   100%
INFO Downloaded file chromInfo.txt.gz looks like a valid gzip'ed file
INFO Downloading https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13
[==================================================]   100%
INFO Downloading https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?save=file&db=nuccore&report=fasta&id=251831106
INFO (server did not tell us the file size, no progress bar)
INFO Downloading http://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
[==================================================]   100%
INFO Building ReferenceDictionary...
Exception in thread "main" java.lang.IllegalArgumentException: Multiple entries with same key: 25=16569 and 25=16571
        at com.google.common.collect.ImmutableMap.checkNoConflict(ImmutableMap.java:190)
        at com.google.common.collect.RegularImmutableMap.checkNoConflictInKeyBucket(RegularImmutableMap.java:109)
        at com.google.common.collect.RegularImmutableMap.fromEntryArray(RegularImmutableMap.java:95)
        at com.google.common.collect.ImmutableMap$Builder.build(ImmutableMap.java:357)
        at de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder.build(ReferenceDictionaryBuilder.java:115)
        at de.charite.compbio.jannovar.impl.parse.ReferenceDictParser.parse(ReferenceDictParser.java:127)
        at de.charite.compbio.jannovar.datasource.JannovarDataFactory.build(JannovarDataFactory.java:101)
        at de.charite.compbio.jannovar.cmd.download.DownloadCommand.run(DownloadCommand.java:43)
        at de.charite.compbio.jannovar.Jannovar.main(Jannovar.java:74)

It seems to be the same bug that is raised here, but it does not look like they are really maintaining jannovar anymore. Any advice on how to proceed?

[Pierre Lindenbaum]

known unresolved issue: https://github.com/charite/jannovar/issues/550

[curious]

Thanks, I referred to that issue in the post