asivache e4acd14675 Now GenomicMap maps (and RemapAlignment outputs) regions between intervals on the master reference as 'N' cigar elements, not 'D'. 'D' is now used only for bona fide deletions. ... Also: do not die if alignment record does not have NM tags (but mapping quality will not be recomputed after remapping/reducing for the lack of required data) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1411 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-11 21:10:17 +00:00
..
CircularArray.java	helper class. array-like random access and fast shift. good for sliding windows (e.g. keeping coverage over last 100 bases while sliding along the reference)	2009-06-09 00:11:57 +00:00
CountedObject.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
CountedObjectComparatorAdapter.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
GenomicMap.java	Now GenomicMap maps (and RemapAlignment outputs) regions between intervals on the master reference as 'N' cigar elements, not 'D'. 'D' is now used only for bona fide deletions.	2009-08-11 21:10:17 +00:00
GenotypingCallStats.java	minor update in report printout format	2009-05-22 13:56:09 +00:00
IndelLikelihood.java	Added a ROD (SangerSNP) for parsing the Sanger's chr20 pilot1 SNP calls.	2009-06-29 16:32:12 +00:00
Interval.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
SimpleInterval.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
TrioConcordanceRecord.java	updated	2009-05-22 17:25:50 +00:00
WhitespaceTextFileParser.java	Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...	2009-05-28 20:13:01 +00:00