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12 Commits (39a47491a94a0e8de2783950d6480255213eb10f)

Author SHA1 Message Date
ebanks a7c306f757 -deal with offsets that can be -1 
-added option to have "D"s inserted for deleted bases in pileup strings


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1635 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-16 16:44:57 +00:00
depristo 4f7ed69242 toString() implemented 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1472 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-28 01:03:58 +00:00
hanna 21d1eba502 Cleaned division of responsibilities between arguments to map function. Reference has been changed 
from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 21:01:37 +00:00
jmaguire 4f6d26849f Behold MultiSampleCaller! 
Complete re-write of PoolCaller algorithm, now basically beta quality code. 

Improvements over PoolCaller include:

	- more correct strand test
	- fractional counts from genotypes (which means no individual lod threshold needed)
	- signifigantly cleaner code; first beta-quality code I've written since BaitDesigner so long ago.
	- faster, less likely to crash!	




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1020 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-16 20:03:24 +00:00
kiran b0cc763eb5 Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@969 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-10 17:31:00 +00:00
depristo 13be846c2a qualsAsInt argument for Pileup -- fixing stupid bug [again] 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@898 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-04 18:52:12 +00:00
depristo 97c8ff75dd qualsAsInt argument for Pileup -- fixing stupid bug 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@897 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-04 18:51:17 +00:00
depristo 9de3e58aa8 qualsAsInt argument for Pileup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@896 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-04 18:37:39 +00:00
depristo dc17a5661d Better accessors for dealing with second base prob pileups 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@785 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-21 22:25:16 +00:00
kiran dac76f041b Added some methods to retreive the probability distributions of individual bases. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@484 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-21 22:26:25 +00:00
depristo 24722a442e Slight code cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 22:21:36 +00:00
depristo 72a3d84ed2 General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 22:13:10 +00:00