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picard-tools-1.53.zip 2011-09-26 31.6 MB 11 weekly downloads
README.txt 2011-09-26 1.5 kB 11 weekly downloads
Picard Release 1.53 26 September 2011 - ReorderSam.java: Get mate reference index before changing header on SAMRecord, in case input is SAM format and reference index is found by looking up reference name in header. - SAMSequenceDictionary.java: Added getReferenceLength method to sum the lengths of the sequences in the dictionary. - SAMRecord.java: Add notes about lack of validation when values are set into SAMRecord. - Add mechanism for converting a SAMRecord to SAM-text format, without having to write a SAM file. Patch courtesy of Fred Long. - CollectRnaSeqMetrics.java: If rRNA.interval_list has not been provided, write empty values for RIBOSOMAL_BASES and PCT_RIBISOMAL_BASES rather than 0. - IlluminaBasecallsToSamConverter.java: Small change to output the "BC" tag with the barcode read sequence, but into the unmatched read file only. - Add Bzip2 support to Picard. - CollectAlignmentSummaryMetrics.java: modified chimerism % calculation so that the denominator is only those reads considered as possible chimeras (was all hq pf reads) - EstimateLibraryComplexity.java: Fix bug in which, if read names were not standard Illumina syntax, all dupes were considered to be optical dupes, and thus library complexity could not be estimated. - IlluminaBasecallsToSam refactor: Removed support for Bustard 1.1. - EstimateLibraryComplexity.java: Initialize PairedReadSequence.readGroup to -1 so that no read group is detectable. Fixes ArrayIndexException.
Source: README.txt, updated 2011-09-26