[Samtools-announce] Picard Release 1.37

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

Picard Release 1.37
20 December 2010

- SamRecordIntervalIteratorFactory.java: When not using index, halt 
iteration as soon as a read is seen that is after the last interval 
requested to avoid uselessly reading the entire file.

- Changes to IntervalList to ensure that only intervals defined against 
valid sequences can be loaded from file.

- MetricsFile.read will not throw an exception if the EOF is reached in 
before any metrics are read.  Instead an empty metrics file object is 
returned

- CollectAlignmentSummaryMetrics.java: If no reads are found than an 
empty unpaired category metric is output

- MarkDuplicates.java: The SAM Header is now parsed for libaries in 
order to try to pre-populate the metrics objects because otherwise there 
would be no duplication metrics objects for a library if no reads were found

- build.xml: Fix dependencies for package-commands target.

- Change behavior of RevertSam so that if 
REMOVE_DUPLICATE_INFORMATION=false, then the output can have records 
with the duplicate flag set despite being unaligned.

- CollectAlignmentSummaryMetrics.java: Reads shorter than 
ADAPTER_MATCH_LENGTH are not considered adapters.
Fixes ArrayIndexOutOfBoundsException from samtools-dev when 0-length read

-Alec