SamReaderFactory doesn't buffer the index SeekablePathStream

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http://samtools.github.io/htsjdk/

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SamReaderFactory doesn't buffer the index SeekablePathStream #1388

Open lbergelson opened 5 years ago

lbergelson commented 5 years ago

Currently when creating a SamReader with SamReaderFactory the stream that is opened to read from the index isn't buffered. This causes pathologically slow performance when reading from a networked source.

We need to add a buffer.