Download Picard 1.111 software

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Java tool that lets you work with BAM files

Whats new in version 1.111:

• Added more possible actions to IntervalListTools, these actions are also supported by a richer IntervalList class
• CommandLineParser.java: Better helpdoc from enums
• First implementation of a rapid-gather tool for BAM files (GatherBamFiles)
• Added flag to CheckIlluminaDirectory to have it create symlinks to the single X Ten locs file for each tile
• IntervalList.java: Concatenate only unique names when merging intervals
• LineReader.java: made LineReader @closeable
• IndexFactory.java: Tabix indices are block-compressed files
• SAMTag.java: Add BC tag
• Speed up adapter-finding code, which is used in IlluminaBasecallsToSam, IlluminaBasecallsToFastq, and MarkIlluminaAdapters. By default, adapter sequences will be truncated at 30 characters, and any adapter pairs that become duplicates as a result are folded together. After 100 adapters have been identified in reads, the list of adapter candidates is pruned down to the one adapter pair that was most frequent among the 100 reads with adapter seque...