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picard-tools-1.45.zip 2011-05-09 10.2 MB
README.txt 2011-05-09 1.6 kB
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Picard release 1.45 9 May 2011 - changes to avoid NPE when calling equals() method on SAMRecord - New program CollectCDnaMetrics -- beta release - Simplified CollectAlignmentSummaryMetrics.java and added PF_ALIGNED_BASES, and PF_MISMATCH_RATE to AlignedSummaryMetrics, CollectAlignmentSummaryMetrics. - BAMRemoteFileTest.java: Move location of HTTP-accessed BAM from SourceForge web to Broad web, because SF doesn't serve this file reliably (perhaps because BAM is GZIP-encoded?) - CollectAlignmentSummaryMetrics.java, MeanQualityByCycle.java, QualityScoreDistribution.java: Ignore non-primary alignments when gathering metrics. - Refactored AbstractTextFileParser, TabbedTextFileParser, and BasicTextFileParser as AbstractInputParser, TabbedInputParser, and BasicInputParser. All now have additional constructors that take InputStreams, and the old constructors that take Files are still there. Except for the name change, they should continue to work the same as before. - ExtractIlluminaBarcodes.java: Fixed Option for BASECALLS_DIR - CollectAlignmentSummaryMetrics.java: Fixed PF_HQ_ERROR_RATE, overflow error due to previous simplification of CollectAlignmentSummaryMetrics.java - RevertSam.java: Do not copy non-primary alignments into reverted SAM. - CommandLineProgram.java: Added an output of the elapsed time when a program ends. - Changes to ensure that cleanup() is called on all instances of SortingCollection and SortingLongCollection after use, to ensure that temporary files are cleaned up ASAP. - SeekableHTTPStream.java: Allow FTP as well as HTTP URL connection (patch courtesy of Lance Frohman).
Source: README.txt, updated 2011-05-09