Mark DePristo b06074d6e7 Updated SortingVCFWriterBase to use PriorityBlockingQueue so that the class is thread-safe ... -- Uses PriorityBlockingQueue instead of PriorityQueue -- synchronized keywords added to all key functions that modify internal state Note that this hasn't been tested extensivesly. Based on report: http://getsatisfaction.com/gsa/topics/missing_loci_output_in_multi_thread_mode_when_implement_sortingvcfwriterbase?utm_content=topic_link&utm_medium=email&utm_source=new_topic		2012-01-13 09:33:16 -05:00
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alignment	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
analyzecovariates	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.	2011-10-27 14:17:07 -04:00
commandline	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
gatk	Added "unbiased" downsampling parameter to PrintReads	2012-01-12 16:33:55 -05:00
jna	Updates to JobRunners from the Queue developer community and from running the WholeGenomePipeline:	2011-08-22 15:13:27 -04:00
queue	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
utils	Updated SortingVCFWriterBase to use PriorityBlockingQueue so that the class is thread-safe	2012-01-13 09:33:16 -05:00