Picard release 1.91
6 May 2013
- Have HttpUtils and HTTPHelper set URLConnection.setDefaultUseCaches(false)
- Introduced new options on IlluminaBasecallsToSam and IlluminaBasecallsToFastq to optionally disable Illumina-style EAMSS filtering.
- Disallow 0-length CIGAR element.
- ExtractIlluminaBarcodes: Don't assert that basecalls directory is writable, just output directory, which may or may not be the same.
- SamToFastq: Allow for interleaved fastq files.
- Change to SeekableBufferedStream to implement skip() directly by either positioning ahead in the buffer or seek()ing instead of relying on InputStream.skip() which reads through the entire skip.
- GenotypeLikelihoods.java: Bug fix when converting (double) GLs into integer PLs: code was saturating at Short.MAX_VALUE = 32767. This is an issue with large events or when very high depth where PLs will be incorrect and saturate to this value.
- SamToFastq: Producing the right result if INTERLEAVE=false and SECOND_END_FASTQ is not null.