| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| picard-tools-1.46.zip | 2011-05-23 | 10.3 MB | |
| README.txt | 2011-05-23 | 1.4 kB | |
| Totals: 2 Items | 10.3 MB | 0 | |
Picard release 1.46 23 May 2011 - SeekableHTTPStream.java: Revert change to support FTP URLs because they aren't seekable. - New program CollectRnaSeqMetrics.java. - SAMRecord.java: Added SAMRecord.getReferencePositionAtReadPosition. - TabbedTextFileWithHeaderParser.java: added ability to retrieve full (non-split) line from Row. - Added option of providing a header array to TabbedTextFileWithHeaderParser. - Fix bug in BasicInputParser where getCurrentLine and getCurrentLineNumber methods return information about the *next* line rather than the current one. - AbstractInputParser.java: Printing out offending line when parser fails. - HsMetricsCalculator.java: Fix for a bug in calculating the HS_PENALTY_nnX numbers that was triggered if the input sequence data provided massively more coverage than needed to cover 80% of targets at nX. In cases where the coverage was below, at or modestly above target coverage levels this wasn't a problem. - FixMateInformation.java: Fix to correctly rename bam index file along without bam output when creating index. - Changes to CollectGcBias metrics to remove a number of poorly tested and documented summary metrics and replace them with two new ones called AT_DROPOUT and GC_DROPOUT that mirror the metrics produced by Illumina. - Allow for other AdapterPairs in ClippingUtility than just the ones defined in IlluminaUtil.