Added documentation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3117 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotator.java

@@ -31,6 +31,37 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
 
+/*
+ General documentation - todo put this in wiki?
+
+ The GenomicAnnotator
+
+ Input Files:
+   - Input files are specified using the -B<name>,<type>,<file path> arg.
+
+   - One of the -B args should have the <name> "variants" and contain the genotypes to be annotated.
+
+   - Data files are also provided using the -B arg and should have <type> be "table".
+     Table format:
+        - the coordinates must be position-based rather than offset-based (eg. 1-based half-open)
+        - special rows:
+            - can contain comment lines starting with #
+            - at the top of the file, there must be a header line of the form:
+              HEADER  columnName1 columnName2 etc.   TODO finalize this
+        - special columns:
+            - first column must be of the form chr:pos or chr:start-end.
+            - alt/ref haplotypes:
+                  - if there is a column named "hap_ref", a variant will only be annotated with a given row if that row's "hap_ref" allele exactly matches the variant's reference sequence.
+                  -
+
+
+
+
+
+
+
+
+ */
 
 /**
  * Annotates variant calls with context information.  Users can specify which of the available annotations to use.