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Author SHA1 Message Date
bthomas 374c0deba2 Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4711 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-19 19:59:05 +00:00
hanna 861ee3e37a Changing testing framework from junit -> testng, for its enhanced configurability. 
Initial test to see how Bamboo will respond.  More detailed email to follow.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4609 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-01 21:31:44 +00:00
bthomas 96cccafb0d Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 
-- getToolkit().subContextFromSampleProperty(): filters a VariantContext to genotypes that come from samples that have a given property value
-- getToolkit().getSamplesWithProperty(): gets all samples with a given property
-- getToolkit().getSamplesFromVariantContext(): sample objects that are referenced by name in a VariantContext



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4361 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 02:16:25 +00:00
bthomas c6c6d32b46 Quickly adding a new convenience method for retreiving a group of samples. The method is getSamples(Collection<String>) and returns a set of sample objects. There's also a test there. 
Ryan is using this to modify VCF code today...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4303 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-17 15:55:17 +00:00
bthomas f66ef4626e Fixing two minor issues: 1) adding a new error message if the user adds a fasta file in a directory that doesn't exist; 2) renaming my sample unit tests so they actually run. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4299 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-16 20:45:51 +00:00
bthomas e5f81d25d4 Adding the --sample-metadata (-SM) command line argument and associated functionality. This is something Matt and I have been working on for a while. Basically, it allows you to integrate sample metadata into an analysis, by including a sample file. More detailed documentation is on the wiki: http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Sample_data_to_an_analysis 
This commit adds two important classes: Sample, which contains data about one sample; and SampleDataSource, which manages sample data a la ReferenceDataSource and ReadsDataSource. 

This code should be stable, but it has not been integrated with existing walkers yet. That's the next commit. 

In the meantime, feel free to experiment with the code - there are two basic example walkers in the playground.sample package. And PLEASE let me know if you see any errors/inconsistencies.

Note that this also adds a new dependency on SnakeYaml, a YAML parser.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4285 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-15 11:50:22 +00:00