--- a/README.md	Mon May 02 17:27:10 2016 -0400
+++ b/README.md	Wed Jul 06 07:01:07 2016 -0400
@@ -1,4 +1,6 @@
-# bcftools (v1.2)
+# bcftools (v1.3)
+
+Copied from branch bcftools1.2:
 
 This aims to be a "faithful" rendering of the bcftool suite. I.e. options are
 presented essentially as closely to the command line version as is useful. 
@@ -7,15 +9,60 @@
 tools (e.g. "intersect", "union" and "complement" being separate tools instead
 of all of them included in the "isec" tool,) please feel free to file an issue.
 
+Updated for bcftools v1.3
+
+This was extended from the bcftools1.2 branch then greatly hand edited to 
+group params and manage param innteractions.
+
+In the macros.xml there are macros and tokens to handle file input and output.  
+These use the datatypes currently available in galaxy: Vcf and Bcf
+The macros take care of bgzip and indexing of inputs.  
+
+The convert command was split into 2 tools, "convert to vcf" and "convert from vcf"
+
 ## TODO:
 
-- Galaxy needs datatypes for bcf and vcf files, block-gzipped and uncompressed.
-- Galaxy needs to automatically index those files with tabix
+- stats needs a matplotlib tool dependency  and pdflatex for generating a pdf of plots
+- cnv needs a matplotlib tool dependency for generating images, then a means to consolidate those.
+- cnv needs an input.vcf for testing, runs with bcftools cnv -s "HG00101" -o 'HG00101/' -p 5 mpileup.vcf
+- roh needs a more useful input.vcf for testing
+- plugin color chrs
+- plugin frameshifts 
 
-## "Complete" Wrappers
+## Status
 
 The wrappers were automatically generated in bulk. That doesn't get them 100%
 of the way there (e.g. meaningful test cases), so the rest of the process is a
 bit slower.
 
-- bcftools call
+- [x] annotate
+- [x] call
+- [ ] cnv (needs real test data, needs plotting)
+- [x] concat
+- [x] consensus
+- [x] convert from vcf
+- [x] convert to vcf
+- [x] filter
+- [x] gtcheck
+- [x] isec
+- [x] merge
+- [x] norm
+- [x] query
+- [x] query list samples
+- [x] reheader
+- [x] roh
+- [x] stats (needs plotting)
+- [x] view
+- [ ] +color chrs
+- [x] +counts
+- [x] +dosage
+- [x] +fill an ac
+- [x] +fill tags
+- [x] +fixploidy
+- [ ] +frameshifts
+- [x] +impute info
+- [x] +mendelian
+- [x] +missing2ref
+- [x] +setgt
+- [x] +tag2tag
+- [x] +vcf2sex