gatk-3.8

Author	SHA1	Message	Date
andrewk	bef475778f	- Updated --hapmap switch to --hapmap-chip to reflect the data being chip data for an individual rather than population allele frequency data in Hapmap - Corrected some bugs to get metrics logging working - Added a switch --force_1base_probs to ignore 4-base probalities if they exist git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@287 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-03 17:32:31 +00:00
andrewk	e3ac0cb500	- A lot of code cleaned up; separated metrics code from AlleleFrequencyMetricsWalker into AlleleMetrics and eliminated the former class. AFMW (aside from being a name so long that it warrants an acronym) can now be implemented by passing an option to AlleleFreqeuncyWalker that logs metrics to a file. - AlleleMetrics and AlleleMetricrsWalker are now ready to take a list of clasess that implement the AllelicVariant interface - Switched a genome location in AlleleFrequencyEstimate from String to GenomeLoc which makes way more sense. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@280 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-03 02:09:10 +00:00

Author

SHA1

Message

Date

andrewk

- Updated --hapmap switch to --hapmap-chip to reflect the data being chip data for an individual rather than population allele frequency data in Hapmap

- Corrected some bugs to get metrics logging working
- Added a switch --force_1base_probs to ignore 4-base probalities if they exist


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@287 348d0f76-0448-11de-a6fe-93d51630548a

2009-04-03 17:32:31 +00:00

andrewk

e3ac0cb500

- A lot of code cleaned up; separated metrics code from AlleleFrequencyMetricsWalker into AlleleMetrics and eliminated the former class. AFMW (aside from being a name so long that it warrants an acronym) can now be implemented by passing an option to AlleleFreqeuncyWalker that logs metrics to a file.

- AlleleMetrics and AlleleMetricrsWalker are now ready to take a list of clasess that implement the AllelicVariant interface
- Switched a genome location in AlleleFrequencyEstimate from String to GenomeLoc which makes way more sense.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@280 348d0f76-0448-11de-a6fe-93d51630548a

2009-04-03 02:09:10 +00:00

2 Commits (c1abcfb0144ed3f6910dec576a593c3f36c4d020)