Adds a buffer to the index stream #1348
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…eading the index over a network possible, fixes #1175
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@lbergelson can you take a look? |
lbergelson
approved these changes
Jul 31, 2019
| @@ -448,6 +484,7 @@ public IntervalList getLociToGenotype(final Collection<Fingerprint> fingerprints | |||
| // Now go through the data at each locus and figure stuff out! | |||
| for (final SamLocusIterator.LocusInfo info : iterator) { | |||
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| log.debug("At locus " + info.toString()); | |||
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This will do a pointless string combine at each position which could be kind of expensive if you don't want this output. If there's a way check if we're in debug mode first than I would test that before doing the debug command.
| @@ -402,7 +438,7 @@ public IntervalList getLociToGenotype(final Collection<Fingerprint> fingerprints | |||
| final SamReader in = SamReaderFactory.makeDefault() | |||
| .enable(SamReaderFactory.Option.CACHE_FILE_BASED_INDEXES) | |||
| .referenceSequence(referenceFasta) | |||
| .open(samFile); | |||
| .open(samFile, null, seekableChannelFunction); | |||
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I would add a comment here describing why this is needed and pointing at the htsjdk issue number ( is there one... there should be.)
…e an unrelated failure...
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This makes reading the index over a network possible, which in turn, fixes #1175.
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