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picard-tools-1.108.zip 2014-02-24 47.0 MB 22 weekly downloads
README.txt 2014-02-24 3.3 kB 11 weekly downloads
Picard release 1.108 24 February 2014 - Handle mix of paired and unpaired reads in MarkIlluminaAdapters, MergeBamAlignment and SamToFastq. - Deprecated "is paired" argument in MergeBamAlignment. - Added "unpaired record output" argument to `SamToFastq`, which emits unpaired reads to its own fastq, if set. - Support Illumina RTA2 (i.e. NextSeq) format for all programs that use IlluminaDataProviderFactory, i.e. IlluminaBasecallsToSam, IlluminaBasecallsToFastq, ExtractIlluminaBarcodes, CheckIlluminaDirectory. - Implement async I/O for writing bgzipped VCFs. This can be enable programmatically, or by passing -Dsamjdk.use_async_io=true to the java command. - BasicFastqWriter.java: Use BufferedOutputStream. Buffer size is controlled by system property samjdk.buffer_size. - BlockCompressedInputStream.java: By default BlockCompressedInputStream wants to ensure that the InputStream it is wrapping is buffered, by buffering if necessary. For certain operations it's critical that buffering not be added, so added new constructor that allows the caller to force no buffering. - libIntelDeflater.so: Mark library as not requiring executable stack. Hopefully this will eliminate warnings that have been reported by some users. - Improved MarkIlluminaAdapters to clip for multiple different adapter sequences in one pass and correct progress logging and metrics that were only counting one read out of each pair. - Minor change so that VCFFileReader.getSequenceDictionary() does not require the VCF to be indexed. - Changed so that the VCFReader doesn't require the presence of an index since MakeSitesOnlyVcf doesn't use it anyway. - TabixUtils.java: Added utility code to pull out the sequence dictionary from a tabix index file. Useful for quickly validating consistency of the sequence dictionary. - VariantContext.java, AbstractVCFCodec.java: Fixed a race condition causing occasional errors in AD and PL fields in multithreaded mode. Removed the side-effect of decoding genotypes when calling VariantContext.toString(). - VariantContextWriterFactory.java: Identify extensions .gz, .bgz, .bgzf as block-compressed vcf when writing VCF. Add methods to create vcf, bcf, and block-compressed vcf explicitly as an alternative to determining format by examining file extension. - Fixed BCF2Utils.toList() to account for the possibility that the input may be an array. - VariantContext.java: Muliple alt alleles were being returned in arbitrary order from subContextFromSamples. This change ensures original order. - VcfFormatConverter.java: Changed the way the CREATE_INDEX option is handled so that it is additive to the DEFAULT_OPTIONS and does not wipe out other default options for VCF writing. - Changed the way MakeSitesOnlyVcf handles index creation options so that it respects other default VCF writing options. - Added a new pair of options to RevertSam to allow for "Sanitizing" SAM and BAM files during revert operations. When fully reverting and sorting by query mode this will optionally discard reads who's pairing information is non-sensical including: a) paired reads who's mates are not present in the file, b) non-paired reads that are duplicated in the file and c) reads marked as paired by not having a single R1 and R2 present. - IntervalListTools.java: Require at least one input file
Source: README.txt, updated 2014-02-24