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