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14 Commits (8a725b6c93540b9b8bf12173ea3964028047dd05)

Author SHA1 Message Date
depristo 8a725b6c93 Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 23:27:55 +00:00
hanna c1e53d407d The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 
unicode quote characters embedded in it.  These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset.  Fixed.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 15:26:32 +00:00
hanna 818a95ea6e Test of new copyright message without unicode characters. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3200 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 14:14:54 +00:00
hanna 1bc26f69e9 An attempt to cleanup the Utils directory. Email to follow. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 23:00:08 +00:00
aaron 790d2a7776 adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2918 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 15:56:44 +00:00
hanna 23d96b1d43 Help system content for the alignment module. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2322 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 16:01:25 +00:00
hanna 4837fe919c Convenience changes. If no -BWT option is specified, pull the BWT location from the reference. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2130 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-23 22:46:05 +00:00
hanna c9c4999354 BWA: odds and ends. Get rid of some spurious debug code that was accidentally 
checked in.  Add a better way to write out unmapped reads (thanks Kiran!)  Add 
a pre-built version of the shared library to the repository for early adoption.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2111 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-22 15:26:07 +00:00
hanna a78bc60c0f Minor tweak to improve ease-of-use of iterator system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2104 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 18:24:19 +00:00
hanna 4fbb6d05d0 Refactoring. Push the revisions to the common aligner interface down into 
the aligner base classes.  Hack the managed implementation to support the
new interface.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-20 17:08:09 +00:00
hanna a95302fe98 Single alignment generator, another checkpoint. Does generate single alignments, but some of the data still 
needs to plumbed through and it may leak memory.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2095 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 21:20:03 +00:00
hanna a972b2769f Checkpoint. Add first phase of single alignment interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2094 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-19 19:03:43 +00:00
hanna ce5034dc5d Finally reinstate the iterator-style interface. Get rid of some scaffolding code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2052 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-16 02:34:19 +00:00
hanna 15c14add4d Repackage the aligner for better partitioning. The C aligner, for example, is now 
partitioned from the Java aligner, and both are partitioned from the more general-
purpose BWT reader.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2045 348d0f76-0448-11de-a6fe-93d51630548a
 2009-11-13 22:55:27 +00:00