Picard release 1.118 28 July 2014 - Fixed index out of bounds exception in CollectTargetedPcrMetrics.
- Get IntelDeflater working again -- had been disabled since package name change. - Genotype.java: Add a function to determine if a genotype is heterozygous non-reference (e.g. C/T if the reference is A) - HardyWeinbergCalculation.java: Fixed HW statistic overflow at large sample numbers. - Update TribbleIndexedFeatureReader.java, TabixReader.java, and TabixFeatureReader.java to add new constructor with given index file. Update AbstractFeatureReader.java to pass index file forward to specific readers. Pass index file in AbstractFeatureReader to underlying readers. - Fixed race condition where synchronouslyClose() would be called multiple times if AbstractAsyncWriter.close() called twice simultaneously. Allowing close() to be called multiple times as per java.io.Closeable interface specifications. - FastqReader: added constructor, toString, removed extra-line. - Add constructor in VCFFileReader that allows to specify the index resource. - Fix problem with open TabixReader after calling close() on the TabixFeatureReader. - Fix signature of CloserUtil.close(List) so that is it more likely to be invoked. - When querying for a contig which doesn't exist in SAMFileReader, return an empty iterator. This matches the behavior in BAMFileReader. -Alec ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
