[Samtools-help] Picard release 1.40

[Alec W. <al...@br...>]

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.


-Alec