hanna b6ecc9e151 Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out ... and the data backing it up deleted without my knowledge. Unfortunately, since the data was deleted, I had to regenerate the data and a new md5. Hopefully the aligner output is still correct. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2493 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-02 20:19:14 +00:00
..
Makefile	Repackage the aligner for better partitioning. The C aligner, for example, is now	2009-11-13 22:55:27 +00:00
build_linux.sh	Checkpoint. Add first phase of single alignment interface.	2009-11-19 19:03:43 +00:00
build_mac.sh	BWA/C changes have arrived in svn repository. Remove temporary storage from Sting repository.	2009-11-11 16:48:21 +00:00
bwa_gateway.cpp	Finishing off data transfer conduits for single alignment generator.	2009-11-20 15:21:59 +00:00
bwa_gateway.h	Finishing off data transfer conduits for single alignment generator.	2009-11-20 15:21:59 +00:00
libbwa.so.1	Add a Unix-standard version number to the file.	2009-11-23 20:07:17 +00:00
org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp	Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out	2010-01-02 20:19:14 +00:00
org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h	Refactoring. Push the revisions to the common aligner interface down into	2009-11-20 17:08:09 +00:00