gatk3的最后一个经典版本3.8

Khalid Shakir 5793625592 No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice. ... 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.		2012-01-08 12:11:55 -05:00
public	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00
settings	SnpEff 2.0.5 support. Re-enabled SnpEff in the HybridSelectionPipeline.	2012-01-03 15:18:36 -05:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00
ivy.xml	No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.	2012-01-08 12:11:55 -05:00