Picard release 1.113
5 May 2014
NOTE: This is the last release that will be based on source code in the Sourceforge repository. The next release will use GitHub. However, binary distributions will continue to be done via Sourceforge.
- SecondaryAlignmentFilter.java: Addition of a simple SamRecordFilter that filters out secondary alignments but not supplementary records.
- Changes to SamLocusIterator to a) check the mapping quality only once per sam record instead of at every base and b) add the ability to filter out non-PF reads during pileup construction.
- First version of CollectWgsMetrics a program that calculates metrics for evaluating whole genome shotgun sequencing experiments.
- RevertOriginalBaseQualitiesAndAddMateCigar.java: do not check for OQ when we are not reverting OQs.
- VariantContextWriterBuilder.java: Require a reference dictionary for Tribble index-on-the-fly but not Tabix.
- Defaults.java: adding a reference fasta to the Defaults to facilitate CRAM reading/writing.
- VCFEncoder.java: Make two methods public so Hadoop-BAM can use them.
- New program ReplaceSamHeader.
- New program AddCommentsToBam.
- Optimize Illumina BCL reading.
- Fix for CheckIlluminaDirectory when the number of clusters is different per tile