Picard release 1.57
5 December 2011
- The code underlying IlluminaBasecallsToSam and ExtractIlluminaBarcodes is undergoing a major refactoring. Currently these programs can be used in two ways. The old process, involved providing BARCODE information and letting the programs detect the structure of your data via the available QSeqs. The new technique requires that you provide a READ_STRUCTURE, which describes the structure of clusters in a run. IlluminaBasecallsToSam/EtractIlluminaBarcode will then treat input cluster data as if they fit the input structure. Please refer to the documentation for the READ_STRUCTURE in IlluminaBasecallsToSam and ExtractIlluminaBarcodes for more information. Important Note: The old process is still available but will be removed in future releases in favor of the new process.
- Allow empty SEQ field in SAMRecord if FZ tag is present.
- Enable BAMIndexer to write to OutputStream in addition to File.
- BuildBamIndex.java: Close input BAM at end in order to reduce file handle leak in cases where this program is being invoked from inside a larger program.
- FormatUtil.java: Support File fields when loading Metric from file. Support Iso8601Date in order to have date & time metrics.
- Add --version option to command-line programs, and put Implementation-Version into jar manifests. Add program version to preamble printed when program starts.
- BAMRecordCodec.java: Clarify requirements for encode method in javadoc.
- MergeSamFiles.java: Fix bug in MergeSamFiles with USE_THREADING=true. Sometimes not all the records would get to the output. Sometimes program would hang. Sometimes it worked fine.
- MetricsFile.java: Add static method readBean().
- CollectInsertSizeMetrics.java: Eliminate obsolete mention of TAIL_LIMIT from usage message.
- Make SAMRecord.mReferenceIndex and mMateReferenceIndex protected so that subclasses can access these attributes.
- Make SAMTagUtil and SAMRecord attribute methods that take binary tag names public.
- FilterSamReads.java: new class that Filters out mapped or unmapped reads from an INPUT sam/bam file and writes out the remaining reads to the specified OUTPUT sam/bam file.
- added PRINT_READ_CATEGORY option to CollectAlignmentSummaryMetrics.
- Added a line to the insertSizeHistogram.R to allow for '#' signs in sample/library names.