samtools/htsjdk — pull request #62 by mremmert (2014-07-16 13:23:23+00:00)
Title: Pass index file in AbstractFeatureReader to underlying readers

The AbstractFeatureReader class has a constructor, where an index resource can be specified. But this index resource is never forwarded to the underlying TabixFeatureReader or TribbleIndexedFeatureReader. These readers expect that the index is located near the VCF file. But in principle the readers already support an alternative location for the index file.
In this commit I have updated the readers to accept a given index resource that don't have to be neccessarily at the same location as the VCF file.