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DoC
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Keep SNPs and indels separately for batch merging; Add options to DepthOfCoverage to count fragments (to not double-count overlapping reads of same fragment); DepthOfCoverage should now support ReducedReads; Replace recusrion with loop in DoC/package.scala (for lists longer than 5000 elements)
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2012-11-21 15:56:53 -05:00 |
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ClassFieldCache.scala
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Added another utility that can convert to RemoteFiles.
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2012-10-17 20:00:03 -04:00 |
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CollectionUtils.scala
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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EmailMessage.scala
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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.
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2012-01-08 12:11:55 -05:00 |
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EmailSettings.scala
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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Logging.scala
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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PrimitiveOptionConversions.scala
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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QJobReport.scala
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Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running
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2012-08-21 14:44:18 -04:00 |
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QJobsReporter.scala
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Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running
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2012-08-21 14:44:18 -04:00 |
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QScriptUtils.scala
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First implementation of a generic 'bundled' Data Processing Pipeline for germline and cancer.
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2012-10-15 13:49:06 -04:00 |
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ReflectionUtils.scala
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Added explicit @ClassType annotations to @Argument for Option[Int] or Option[Double] since scala seems to change the reflected type to Option[Object] on some systems.
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2012-10-19 13:20:29 -04:00 |
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RemoteFile.scala
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Added more logging to push/pull of RemoteFiles.
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2012-10-17 09:52:17 -04:00 |
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RemoteFileConverter.scala
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Added another utility that can convert to RemoteFiles.
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2012-10-17 20:00:03 -04:00 |
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Retry.scala
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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RetryException.scala
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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ScalaCompoundArgumentTypeDescriptor.scala
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Better error message when generic types are erased from scala collections.
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2012-10-22 16:27:31 -04:00 |
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ShellUtils.scala
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Queue now properly escapes all shell arguments in generated shell scripts
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2011-12-01 18:13:44 -05:00 |
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StringFileConversions.scala
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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.
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2012-01-08 12:11:55 -05:00 |
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SystemUtils.scala
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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.
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2012-01-08 12:11:55 -05:00 |
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TextFormatUtils.scala
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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VCF_BAM_utilities.scala
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Keep SNPs and indels separately for batch merging; Add options to DepthOfCoverage to count fragments (to not double-count overlapping reads of same fragment); DepthOfCoverage should now support ReducedReads; Replace recusrion with loop in DoC/package.scala (for lists longer than 5000 elements)
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2012-11-21 15:56:53 -05:00 |
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