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Allow reference file to be loaded from HDFS or GS #512

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arahuja opened this issue Jul 28, 2016 · 0 comments
Open

Allow reference file to be loaded from HDFS or GS #512

arahuja opened this issue Jul 28, 2016 · 0 comments
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arahuja commented Jul 28, 2016

Currently --reference-fasta gs://genomics-public-data/references/b37/Homo_sapiens_assembly19.fasta.gz

gives

Exception in thread "main" htsjdk.samtools.SAMException: Error opening file: Homo_sapiens_assembly19.fasta.gz
        at htsjdk.samtools.util.IOUtil.openGzipFileForReading(IOUtil.java:518)
        at htsjdk.samtools.util.IOUtil.openFileForReading(IOUtil.java:494)
        at htsjdk.samtools.reference.FastaSequenceFile.<init>(FastaSequenceFile.java:53)

It is possible this failure is due to gzip, but that should work as well.
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