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9 Commits (f39092526dddc24ca3a8e4dec405ef210008078b)

Author SHA1 Message Date
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
depristo 2cd9a1597f Simple improvements to allele caller 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@254 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-02 14:09:14 +00:00
jmaguire ede52f7359 - take command line arguments 
- output GFF lines to a file (specified by a command line argument)
- improve the GFF output string


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@240 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-31 18:43:00 +00:00
jmaguire 875802e8fc print output as a GFF line. 
still need to add printing GFF intervals for stretches of confident reference calls.

does the GFF ROD class handle intervals?? We'll find out. >:)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@225 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-30 17:47:35 +00:00
andrewk 0331cd8e95 Updated AlleleFrequency* classes to calculate separate lods for VarVsRef and BestVsNextBest mixture (qstar) theories; AFWMetrics now reports single sample performance w.r.t. Hapmap chip using the appropriate lod for gentoyping (BestVsNextBest) or variant / reference calling (VarVsRef). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@196 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-26 02:10:18 +00:00
jmaguire 44acc358b7 Add a "notes" member to the AlleleFreqencyEstimate, e.g. for hapmap metadata. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@188 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-25 15:18:10 +00:00
andrewk 30babbf5b9 Restructured AlleleFrequencyMetricsWalker to correctly report Hapmap concordance numbers for genotyping and added reporting for Hapmap reference/variant calling. Also, tiny bugfix in interval code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@181 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-25 01:12:05 +00:00
andrewk 9dee9ab51c Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@163 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 03:58:03 +00:00
hanna 63cd1fe201 Push core / playground lower into the tree. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 23:19:54 +00:00