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Release Notes 2.0.4
Note: If you are a RUM 1.x user and you haven't read the release notes for RUM 2.0.1, please do so. That version contains lots of changes from RUM 1.x.
Between 2.0.3 and 2.0.4 we have addressed some bugs and added a few minor features.
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Change calculation of amount of RAM required so that we request slightly more, in order to fix an issue where parse_blat_out.pl occasionally ran out of memory (#152).
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Fix a slight memory leak in parse_blat_out.pl (#152).
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Fix an issue where sort_RUM_by_location.pl occasionally had temporary file name conflicts among different chunks (#153).
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Fix an issue where RUM was mistakenly flagging some FASTQ input as variable length. This was causing affected jobs to fail completely (#148).
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Change calculation of TLEN field (#147).
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Allow user to specify additional options to qsub using --platform-flags.
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Add the XS:A flag to the SAM file, when available (#127).
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Reduce memory footprint of rum2cov.pl. Very large jobs were running out of memory.