Picard release 1.119
25 August 2014
- Updated AbstractOpticalDuplicateFinder to handle post-CASAVA 1.8 read
names. Pass READ_NAME_REGEX=null to skip optical duplicate detection in
MarkDuplicates.
- Fixed RevertSam to harmonize different quality score encoding schemes
when the sanitize option is set.
- Modified Casava18ReadNameEncoder to correctly display filter status.
- SamPairUtil: Added the ability to set the mate cigar tag on supplementary
alignments. Updated AbstractAlignmentMerger to set mate cigars when merging
supplementary alignments.
- CollectWgsMetrics: Added 2 new metrics- the fraction of bases attaining
15X and 25X coverage respectively.
- Added a new tool, CollectBaseDistributionByCycle, that computes the
nucleotide distribution per cycle.
- FileAppendStreamLRUCache: Added wrapping of FileOutputStreams with
BufferedOutputStreams.
- Fixed a bug in BCF2Writer where it was double-closing the output stream.
- Fixed VariantContext to ignore symbolic alleles when running strict
validation for a VCF.
- MetricsBase: Fixed a NullPointerException
- IndexStreamBuffer: Fixed a bug in which a data-exhaustion error was being
thrown prematurely.
-Brad
--
Brad Taylor
Associate Software Engineer, Genomics Platform
Broad Institute
320 Charles Street, Cambridge MA
617-714-7721
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