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Re: [Samtools-help] Picard release 1.46
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From: mei ge <rge...@ya...> - 2011-05-25 19:15:26
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Hi Alec, I use the CollectRnaSeqMetrics in the new release Picard. I don't know where to get the Ribosomal_intervals file. Can you point a place for the file? Thanks Mei --- On Mon, 5/23/11, Alec Wysoker <al...@br...> wrote: From: Alec Wysoker <al...@br...> Subject: [Samtools-help] Picard release 1.46 To: "samtools help" <sam...@li...>, "samtools-devel" <sam...@li...>, sam...@li... Date: Monday, May 23, 2011, 11:15 AM Picard release 1.46 23 May 2011 - SeekableHTTPStream.java: Revert change to support FTP URLs because they aren't seekable. - New program CollectRnaSeqMetrics.java. - SAMRecord.java: Added SAMRecord.getReferencePositionAtReadPosition. - TabbedTextFileWithHeaderParser.java: added ability to retrieve full (non-split) line from Row. - Added option of providing a header array to TabbedTextFileWithHeaderParser. - Fix bug in BasicInputParser where getCurrentLine and getCurrentLineNumber methods return information about the *next* line rather than the current one. - AbstractInputParser.java: Printing out offending line when parser fails. - HsMetricsCalculator.java: Fix for a bug in calculating the HS_PENALTY_nnX numbers that was triggered if the input sequence data provided massively more coverage than needed to cover 80% of targets at nX. In cases where the coverage was below, at or modestly above target coverage levels this wasn't a problem. - FixMateInformation.java: Fix to correctly rename bam index file along without bam output when creating index. - Changes to CollectGcBias metrics to remove a number of poorly tested and documented summary metrics and replace them with two new ones called AT_DROPOUT and GC_DROPOUT that mirror the metrics produced by Illumina. - Allow for other AdapterPairs in ClippingUtility than just the ones defined in IlluminaUtil. -Alec ------------------------------------------------------------------------------ What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay _______________________________________________ Samtools-help mailing list Sam...@li... https://lists.sourceforge.net/lists/listinfo/samtools-help |