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Reading tabix from ftp #2

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dariober opened this issue May 29, 2016 · 0 comments
Open

Reading tabix from ftp #2

dariober opened this issue May 29, 2016 · 0 comments

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@dariober
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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

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