asivache aadd230636 N-Way-Out is back. Now uses SAMReadID to identify each read's source bam, so should be reliable. Interface is sort of ugly fo now: to generate output file names, .bam is stripped from input file names, then the value of -nWayOut argument is pasted on (and all the output files are written into the current dir). ... Unrelated change: in the sorted-target mode (when we read sorted target intervals one by on from a file), one can now specify multiple semicolon-separated interval files (all must be sorted). Not hugely useful probably, but makes --targetIntervals always process its values in exactly the same way, so we are consistent (it has been already taking ;-separated args in unsorted mode) NwayIntervalMergingIterator: reads in multiple sorted GenomeLoc input streams (iterators) and presents them as a single sorted and merged stream git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4602 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-01 16:06:51 +00:00
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alignment	all fixed..thanks Matt!	2010-09-10 06:18:59 +00:00
commandline	Get rid of the static cache of ArgumentTypeDescriptors by making them an integral part of the	2010-10-27 19:44:55 +00:00
datasources/pipeline	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00
gatk	Users can now use VariantAnnotator to add annotations from one VCF to another. For example, if you want to annotate your target VCF with the AC field value from the rod bound to CEU1kg, you can specify -E CEU1kg.AC and records will be annotated with CEU1kg.AC=N when a record exists in that rod at the given position.	2010-10-29 16:38:31 +00:00
oneoffprojects/walkers	The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder.	2010-09-21 18:21:22 +00:00
playground/gatk/walkers	Recent changes to the build system make the build system complain loudly about	2010-09-24 22:09:12 +00:00
utils	N-Way-Out is back. Now uses SAMReadID to identify each read's source bam, so should be reliable. Interface is sort of ugly fo now: to generate output file names, .bam is stripped from input file names, then the value of -nWayOut argument is pasted on (and all the output files are written into the current dir).	2010-11-01 16:06:51 +00:00
BaseTest.java	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
WalkerTest.java	Parallelized VariantEval. Refactored output to support parallel output style. Minor improvements to testing framework to enable easy executeTestParallel to run -nt 1 and -nt 4 by default.	2010-10-26 20:21:38 +00:00