git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@1 702bc0d3-552f-47ad-8d22-b90160be019a


git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@6 702bc0d3-552f-47ad-8d22-b90160be019a
tested ZackTestWalker

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@7 702bc0d3-552f-47ad-8d22-b90160be019a
Bad package path name.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@8 702bc0d3-552f-47ad-8d22-b90160be019a
First checked in under this path. Reverse strand still isn't working correctly.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@9 702bc0d3-552f-47ad-8d22-b90160be019a
initial checkin of base-cycle-quality walker



git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@10 702bc0d3-552f-47ad-8d22-b90160be019a
added labels to base quality walker csv output (ex postAlignment). label is passed in as cmd line arg.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@11 702bc0d3-552f-47ad-8d22-b90160be019a
basic nmer count walker. only has raw counts per unique nmer of a specified length

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@12 702bc0d3-552f-47ad-8d22-b90160be019a
refactored qcmetrics walker packaging



git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@13 702bc0d3-552f-47ad-8d22-b90160be019a
Restoring my most recent unchecked in version.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@14 702bc0d3-552f-47ad-8d22-b90160be019a
Fixed some strand issues.  Seems to be roughly working now.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@15 702bc0d3-552f-47ad-8d22-b90160be019a
Base utils that aren't in the main gatk class.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@16 702bc0d3-552f-47ad-8d22-b90160be019a
Made tree reducible for parallelization.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@17 702bc0d3-552f-47ad-8d22-b90160be019a
Made the cytosine walker a base class.  Only cytosines get reduced by subclasses.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@18 702bc0d3-552f-47ad-8d22-b90160be019a
MethLevelWalker is working with single thread, it still throws an exception in multi-threaded mode.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@19 702bc0d3-552f-47ad-8d22-b90160be019a
Now it works with multiple threads.  The problem was actually in the CpgSummarizer in genomeLibs.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@20 702bc0d3-552f-47ad-8d22-b90160be019a
A template to make new cytosine walkers.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@21 702bc0d3-552f-47ad-8d22-b90160be019a
Removed some unnecessary imports.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@22 702bc0d3-552f-47ad-8d22-b90160be019a
Added some utility functions.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@23 702bc0d3-552f-47ad-8d22-b90160be019a
Changed to use CpgBackedByGatk rather than a plain Cpg.  Cpg has no chrom information.

git-svn-id: https://svn.code.sf.net/p/uecgatk/code/trunk@24 702bc0d3-552f-47ad-8d22-b90160be019a