Command download broken #550
Description
Describe the bug
There is problematic data with chrM vs chrMT.
To Reproduce
+-> java -jar jannovar-cli/target/jannovar-cli-0.40-SNAPSHOT.jar download -d hg19/refseq
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 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
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
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
INFO Downloading https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?save=file&db=nuccore&report=fasta&id=251831106
INFO Downloading http://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
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:139)
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)
Expected behavior
The download and build should succeed.
Additional context
N/A