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picard-tools-1.52.zip 2011-08-29 30.6 MB
README.txt 2011-08-29 2.0 kB
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Picard release 1.52 29 August 2011 IMPORTANT: As of this release, sam.jar (comprising net.sf.samtools packages) requires Java 1.6 or newer. - CloserUtil.java: Make null-safe. - Add IGNORE_SEQUENCE option to CollectRnaSeqMetrics to enable specification of one or more sequences that should not be counted in most of the RNA seq metrics. - AbstractInputParser.java: added flag for skipping blank lines in input files (now the default behavior). - TabbedTextFileWithHeaderParser.java: Added a method to get the column names back. - Metrics that are aggregated at multiple levels now share a common ancestor MultilevelMetrics. - Md5CalculatingInputStream and Md5CalculatingOutputStream now have methods for accessing the md5 hash after they are closed (previously they would only write it to a file). - Modifications to support an ordered list of temp directories in Picard programs. Programs will generally use the list in order until there is insufficient free space in a directory to be sure of completely writing a file there. If all directories run short of space the last directory in the list continues to be used. - IoUtil.java: Added methods for buffered reading and writing of UTF-8 encoded files. - Add way to merge IntervalLists without making hugely long interval names if merging lots of intervals. - Small change to attempt to make any temp directories world readable and writable. - CollectRnaSeqMetrics.java: Change algorithm for determining if a read is rRNA. Now works by looking at overlap of entire fragment with rRNA intervals, rather than base-by-base overlap with rRNA intervals. - Removed AsciiLineReader and AsciiLineReaderImpl as there does not appear to be a performance benefit to their use, now that Java 1.5 is no longer supported. - AbstractInputParser.java: Fix isComment so it does not NPE when encountering a blank line. - SAMBinaryTagAndUnsignedArrayValue.java, SAMBinaryTagAndValue.java: Make these classes public for GATK.
Source: README.txt, updated 2011-08-29