gatk-3.8

Author	SHA1	Message	Date
bthomas	bc12055fcf	Quick patch to fix the sample code. It wasn't actually initializing the sample data source, so I added a call to initializeSampleDataSource() in GenomeAnalysisEngine. I think there was just an error resolving the versions of GenomeAnalysisEngine Also added a new error message that I thought would be helpful... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4301 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-17 14:05:26 +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

Author

SHA1

Message

Date

bthomas

bc12055fcf

Quick patch to fix the sample code. It wasn't actually initializing the sample data source, so I added a call to initializeSampleDataSource() in GenomeAnalysisEngine. I think there was just an error resolving the versions of GenomeAnalysisEngine

Also added a new error message that I thought would be helpful...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4301 348d0f76-0448-11de-a6fe-93d51630548a

2010-09-17 14:05:26 +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

2 Commits (e45b699ac059045f4e762c42b872c42eaf250fb3)