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It appears tabix files from ftp cannot be read. For example, read a vcf file from 1000genomes:
import htsjdk.samtools.seekablestream.SeekableStream;
import htsjdk.samtools.seekablestream.SeekableStreamFactory;
import htsjdk.tribble.readers.TabixReader;
String ftp= "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/input_call_sets/ALL.wex.union_illumina_wcmc_bcm_bc_bi.20110521.snps.exome.sites.vcf.gz";
// Here it hangs:
TabixReader tabix= new TabixReader(ftp);
// In particular, this seems to hang:
SeekableStream stream= SeekableStreamFactory
.getInstance()
.getBufferedStream(SeekableStreamFactory.getInstance()
.getStreamFor(ftp));
Would be good to post on biostars/htsjdk list
The text was updated successfully, but these errors were encountered:
It appears tabix files from ftp cannot be read. For example, read a vcf file from 1000genomes:
Would be good to post on biostars/htsjdk list
The text was updated successfully, but these errors were encountered: