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picard-tools-1.75.zip 2012-08-13 35.6 MB 11 weekly downloads
README.txt 2012-08-13 837 Bytes 11 weekly downloads
Picard release 1.75 13 August 2012 - Added method to make a read unmapped and a method to check whether any cigar element consumes both read and reference bases to SAMUtils; used these methods in AbstractAlignment merger to catch reads with cigar strings that don't consume any read or reference bases (e.g. all soft-clipped) and make them unmapped - Augmented plots for GC Bias Metrics, Mean Quality by Cycle, Quality Score Distribution, and RNA Sequence Coverage. Specifically, if the plot was generated from a read group .bam, the title of the plot includes the read group's library. - IlluminaDataProvider.java: Produce more useful error output by printing out the class of the parser that's failing - Support SeekableStream BAM index. - build.xml: Added single-jar packaging target tasks. Consolidated package-commands task.
Source: README.txt, updated 2012-08-13