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
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
Limitations:
1) Can't handle RC alignments.
2) Can't handle indels.
3) Can't handle N's in reference bases.
4) Stops at first hit.
Ran BWT over a test suite of 800k Ecoli reads. After removing alignments with indels / reads with Ns, the remaining reads were aligned with quality 'equal to' that of the alignment stored in the BAM file. In this case 'equal' quality is <= mismatches to the reference as the existing alignment stored in the BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1710 348d0f76-0448-11de-a6fe-93d51630548a
hanna