htsjdk
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Resolve issues around integrating HTTP NIO provider
Trying to add an http nio provider as a test dependency as part of #1688 caused issues because of some deficiencies in the library.
See the test results here
There are 2 failure types:
- Not implemented exceptions HtsgetBAMCodecTest because of a missing Path.resolveSibling() method
- A failure in SamReaderFactoryTest.testOpenURIFallback() due not falling back for http URLS
example
Gradle suite > Gradle test > htsjdk.beta.codecs.reads.htsget.HtsgetBAM.HtsgetBAMCodecTest > testGetHeader FAILED
java.lang.UnsupportedOperationException: Not implemented
at org.broadinstitute.http.nio.HttpPath.resolveSibling(HttpPath.java:362)
at htsjdk.samtools.SamFiles.lookForIndex(SamFiles.java:71)
at htsjdk.samtools.SamFiles.findIndex(SamFiles.java:38)
at htsjdk.beta.plugin.reads.ReadsBundle.resolveIndex(ReadsBundle.java:167)
at htsjdk.beta.plugin.reads.ReadsBundle.resolveIndex(ReadsBundle.java:147)
at htsjdk.beta.plugin.registry.ReadsResolver.getReadsDecoder(ReadsResolver.java:73)
at htsjdk.beta.codecs.reads.htsget.HtsgetBAM.HtsgetBAMCodecTest.testGetHeader(HtsgetBAMCodecTest.java:47)