Picard release 1.111
7 April 2014
- 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 sequence found. In small tests, this has reduced IlluminaBasecallsToSam execution time by about 40%. Moreover, since in most cases an Illumina lane uses only one adapter pair, pruning the list down to one pair reduces the chance that a read will be incorrectly marked with an adapter pair that was not used in the lane. Note that for IlluminaBasecallsToSam and IlluminaBasecallsToFastq, there is no control over the configuration of this functionality. However, MarkIlluminaAdapters has new command-line options that control all of the above behavior.
- release script no longer copies /picard/trunk to /picard/branches
- VariantContextWriterFactory.java: Add .gzip to BLOCK_COMPRESSED_EXTENSIONS
- CloseableIterator.java: Implement `Closeable` to facilitate try-with-resources in Java 7+ projects that depend on picard.
- CheckIlluminaDirectory.java: Create lane directories for symlinks if they don't exist.
- Merged nh_mate_cigar_refactoring r1775:r1889 into trunk
- VCFCompoundHeaderLine.java: Added support for VCFv4.2 Version tags in header fields.
- New VariantContextWriterBuilder class and tests
- setting ADD_MATE_CIGAR to default to true in FixMateInformation and MergeBamAlignment.