Picard release 1.40
15 February 2011
- CollectMultipleMetrics.java: Made sure that the list of programs to run is unique.
- Faster implementation of MeanQualityByCycle that cuts off about 2/3 of the runtime.
- Adds a .equals method to MetricBase that compares the values for all public fields in the class; modifies MetricFile to have separate comparison methods for header, metrics, and histogram and to call all three of them in the .equals method. FormatUtil now handles Bytes.
- QualityScoreDistribution.java, MetricsFile.java: Fixed to cope with the situation when there are no valid bases in an input sam/bam file.
- Hack to fix strange problem with reading BAM via HTTP from SourceForge.