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gatk-3.8/public/scala/src/org/broadinstitute/sting/queue/util
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Mauricio Carneiro 22d2563823 added BWA SW alignment 
The pipeline now accepts fasta/fastq files and aligns them using BWA SW, adds default basequalities, creates read groups and performs BQSR.
 		2011-08-09 17:05:24 -04:00
..
CollectionUtils.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
CommandLineJob.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
EmailMessage.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
EmailSettings.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
IOUtils.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
JobExitException.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
Logging.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PrimitiveOptionConversions.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ProcessController.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
QScriptUtils.scala added BWA SW alignment 2011-08-09 17:05:24 -04:00
ReflectionUtils.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
Retry.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
RetryException.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ScalaCompoundArgumentTypeDescriptor.scala Updated to reflect new parse() function 2011-07-30 15:34:20 -04:00
ShellJob.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
StringFileConversions.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
SystemUtils.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
TextFormatUtils.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
VCF_BAM_utilities.scala Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00