Commit [r210] Maximize Restore History

Autoaligner

1. Fix regexs to more explicitly match versioned genome, build code, and both paired-end fastq files
2. Modified build code and versioned genome to set as lower case to match case of approved index names
3. Fixed a bug that would print an error to log (saying dir wasn't created) when a new analysis report directory was created
4. Updated server URL for createAnalysisMain to hci-bio-app
5. Fixed logging errors
6. Added more new sequencing application codes
7. Logs now report how each sample is handled
Sample
1. added getters/setters for a number of new booleans

monkeymanstan 2014-01-13

changed /trunk/Source/edu/utah/ames/bioinfo/Autoaligner.java
changed /trunk/Source/edu/utah/ames/bioinfo/Sample.java
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