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Name Modified Size Downloads / Week Status
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picard-tools-1.37.zip 2010-12-20 7.9 MB 0
README.txt 2010-12-20 1.2 kB 0
Totals: 2 Items   7.9 MB
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
Source: README.txt, updated 2010-12-20

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