Picard release 1.90
22 April 2013
- tribble javadoc improvements
- Add TileMetricsUtil to easily get Tile-like objects out of TileMetricsOut.bin
- Have ParsingUtils call getURLHelper, so that registerHelperClass actually does something.
- Have ParsingUtils support FTP out-of-the-box
- Add FTPHelper as an implementation of URLHelper, and RemoteURLHelper which delegates to HTTPHelper and FTPHelper as appropriate. ParsingUtils should now, by default, support FTP. Add additional tests to make sure of this.
- Clients can still register their own URLHelper.
- Fix issues in which net.sf.samtools code depended on net.sf.picard code, and fix build.xml so this doesn't happen again.
- Correct spelling error in error enum value, and switch error regarding adjacent CIGAR I and D to the corrected enum value.
- SAMRecord.java: Add validation of indexing bin if present and appropriate.