depristo
|
7d281296a7
|
Finishing checking for building
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1027 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-06-17 14:12:40 +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 |
andrewk
|
0219d33e10
|
QualityUtils: added reverse function to reverse an array of bytes (and not complement it), BaseUtils: split qualToProb into itself and qualToErrProb, CovariateCounterWalker and LogisticRecalibrationWalker: several changes including a properly acocunting (only partly complete) for reversing AND complementing bases that are negative strand, PrintReadsWalker: created option to output reads to a BAM file rather than just to the sceern (useful for creating a downsampled BAM file)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@770 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-05-21 18:30:45 +00:00 |
kiran
|
68c9455c0f
|
Moved the base complement method to BaseUtils.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@711 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-05-14 18:57:48 +00:00 |
|
kiran
|
64c65c7751
|
New methods to generated compressed SQ quality elements in line with the SAM spec.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@699 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-05-14 16:50:31 +00:00 |
|
depristo
|
71e8f47a6c
|
boundQual function for capping qual values
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@623 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-05-07 18:04:18 +00:00 |
|
depristo
|
1cc5e74435
|
More ways to access quality utils
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@573 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-04-30 22:12:07 +00:00 |
|
kiran
|
59b2e6a90f
|
Added some stuff for retreiving the base index and probability of a compressed base.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@329 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-04-08 15:52:58 +00:00 |
|
kiran
|
ef06924f73
|
JavaDocs!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@290 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-04-03 19:19:17 +00:00 |
|
kiran
|
b854c24575
|
Oops. I gave this method the wrong name first time around.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@283 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-04-03 15:46:26 +00:00 |
|
kiran
|
a8a6c63a32
|
A class with some static methods that aid the manipulation of quality scores and probabilities (including a method to compress a base and quality score into a byte for SAM output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@271 348d0f76-0448-11de-a6fe-93d51630548a
|
2009-04-02 22:06:15 +00:00 |