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From: Alec W. <al...@br...> - 2010-08-18 14:17:12
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Picard Release 1.28 18 August 2010 - In various programs, write messages to stderr rather than stdout, so that BAM output can be sent to stdout. - BlockCompressedFilePointerUtil: encapsulate code for manipulating BGZF virtual file pointers. Make sure it works for virtual file pointer that is so large as to be negative as signed long. - BamToBfq: Added option to write only the first N bases of the read to the bfq file. - CigarUtil: Added method to add soft-clipped bases to either end of a cigar (used when reads have been trimmed before alignment and the cigar needs to be adjusted to reflect this). - AlignmentMerger: Added option to specify reserved tags from alignment bam to bring over when merging. - SamRecord: Change mAttributes from ArrayList to custom linked list to reduce memory footprint. - SamFileValidator: Added some progress logging. - DuplicationMetrics: Change to allow calculation of estimated library size in heavily duplicated (as in 99%+ duplicaiton) data. - MergeBamAlignment: Clarified documentation to make clear that a sequence dictionary is expected in the same directory as the reference fasta and that its extension should be .dict. -Alec |