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picard-tools-1.51.zip 2011-08-15 30.6 MB 0
README.txt 2011-08-15 1.5 kB 0
Totals: 2 Items   30.6 MB
Picard release 1.51 15 August 2011 - Add support for array tag values (type B) for signed and unsigned byte, short, int; and for float. Note that previously byte arrays were stored as hex ascii string (type H). Type H will still be read, but no longer written. The only exception is that if a BAM record containing a tag of H type is read from a file, and none of the variable length part of the BAM record is changed, then if the BAM record is written to another file, the tag will still be H type. - MergeBamAlignment.java: Fix bug triggered when EXPECTED_ORIENTATIONS is not set on the command line. - MergeSamFiles.java: Fix bug created 7/28 in which if input were unsorted, SORT_ORDER=coordinate was ignored. - MergeBamAlignment.java: Add option to disable soft clipping if 3' end of read extends past 5' end of mate. - insertSizeHistogram.R: change script so that spaces are tolerated in sample/library names, columns separated on tabs only. - SAMReadGroupRecord.java: Support FO (flow order) and KS (key sequence) attributes of read group. - meanQualityByCycle.R, qualityScoreDistribution.R: Added tab separator for reading metrics files instead of default whitespace separator, to better handle data that includes sample names which may have spaced in them. - BlockCompressedInputStream.java: Lazily initialize ByteArrayOutputStream so that it is not allocated if readLine is never called. - CollectRnaSeqMetrics.java: Added check that there's actually data in the histogram to plot before calling R.
Source: README.txt, updated 2011-08-15

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