Picard release 1.50
2 August 2011
- Make some methods public so that SAMTextWriter can be used to format SAMRecords as text without having to write a SAM file. Patch courtesy of Matti Niemenmaa.
- BlockCompressedInputStream.java: Implement readLine() method for Tabix. Patch courtesy of Matthias Haimel and Fred Long.
- SamToFastq.java: Skip non-primary alignments by default. If default is overridden, exceptions may result for paired reads with non-primary alignments.
- FastqToSam.java: Add options MIN_Q and MAX_Q to FastqToSam.
- CommandLineParser.java: Eliminate requirement that field annotated with @PositionalArguments must be public.
- Changes to add three new metrics to CollectRnaSeqMetrics - median cv of coverage, 5' bias and 3' bias, all using the top 1000 expressed transcripts.
- MergeSamFiles.java: Add @CO lines to output SAM header regardless of whether output needs to be sorted or not.
- CollectRnaSeqMetrics.java: Added a handful more metrics to RNA metrics: PF_BASES, PCT_USABLE_BASES and MEDIAN_5PRIME_TO_3PRIME_BIAS
- MergeBamAlignment.java: Added the ability to specify queryname as the sort order for final output of MergeBamAlignment. Note that this does not save a sort, as records are internally coordinate-sorted in order to set tags (NM, etc) that require a comparison with the reference. Default behavior is unchanged.
- CollectRnaSeqMetrics.java: Added a plot of normalized position along transcript vs. normalized coverage to the RNA seq metrics.