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QScript accessor to QSettings to specify a default runName and other default function settings. Because log files are no longer pseudo-random their presense can be used to tell if a job without other file outputs is "done". For now still using the log's .done file in addition to original outputs. Gathered log files concatenate all log files together into the stdout. InProcessFunctions now have PrintStreams for stdout and stderr. Updated ivy to use commons-io 2.1 for copying logs to the stdout PrintStream. Removed snakeyaml. During graph tracking of outputs the Index files, and now BAM MD5s, are tracked with the gathering of the original file. In Queue generated wrappers for the GATK the Index and MD5s used for tracking are switched to private scope. Added more detailed output when running with -l DEBUG. Simplified graphviz visualization for additional debugging. Switched usage of the scala class 'List' to the trait 'Seq' (think java.util.ArrayList vs. using the interface java.util.List) Minor cleanup to build including sending ant gsalib to R's default libloc. |
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