From 84825c883438199315670e519b59675a0d84c176 Mon Sep 17 00:00:00 2001
From: Todd J Treangen <treangen@gmail.com>
Date: Mon, 24 Nov 2014 16:22:22 -0500
Subject: [PATCH 1/2] clarify -r and -g parameter usage

---
 docs/content/parsnp/quickstart.rst | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/docs/content/parsnp/quickstart.rst b/docs/content/parsnp/quickstart.rst
index 8a0cf52..cc7f473 100644
--- a/docs/content/parsnp/quickstart.rst
+++ b/docs/content/parsnp/quickstart.rst
@@ -50,12 +50,17 @@ With reference & genbank file::
    
    parsnp -g <reference_genbank_file1,reference_genbank_file2,..> -d <genome_dir> -p <threads> 
    
-NOTE: Genbank files are currently expected to have GI numbers for indexing. This means custom Genbank files (not downloaded from NCBI) will not have annotations appear in Gingr, though the alignment should still work. The dependency on GIs is expected to change in future versions.
+NOTE: 
+
+    1. Genbank files are currently expected to have GI numbers for indexing. This means custom Genbank files (not downloaded from NCBI) will not have annotations appear in Gingr, though the alignment should still work. The dependency on GIs is expected to change in future versions.
+    2. GenBank files can only be specific for the reference genome
+    3. -g and -r are mutually exclusive; you can either provide a fasta file for your reference genome, or GenBank file, but not both.
+    4. All non-reference genomes are captured with the -d parameter. These genomes *must* be in fasta format and located within the specified directory.
 
 With reference but without genbank file::
    
    parsnp -r <reference_genome> -d <genome_dir> -p <threads> 
-
+   
 Autorecruit reference to a draft assembly::
    
    parsnp -q <draft_assembly> -d <genome_db> -p <threads> 

From 4232b3851d9fb689fdc7f11d0af46924a7eff263 Mon Sep 17 00:00:00 2001
From: Todd J Treangen <treangen@gmail.com>
Date: Mon, 24 Nov 2014 16:38:14 -0500
Subject: [PATCH 2/2] Update quickstart.rst

---
 docs/content/parsnp/quickstart.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/content/parsnp/quickstart.rst b/docs/content/parsnp/quickstart.rst
index cc7f473..7c2d1ff 100644
--- a/docs/content/parsnp/quickstart.rst
+++ b/docs/content/parsnp/quickstart.rst
@@ -48,7 +48,7 @@ Parsnp quick start for three example scenarios.
 
 With reference & genbank file::
    
-   parsnp -g <reference_genbank_file1,reference_genbank_file2,..> -d <genome_dir> -p <threads> 
+   parsnp -g <reference_replicon1,reference_replicon2,..> -d <genome_dir> -p <threads> 
    
 NOTE: 
 
@@ -72,7 +72,7 @@ Input/output::
 
    -c = <flag>: (c)urated genome directory, use all genomes in dir and ignore MUMi? (default = NO)
    -d = <path>: (d)irectory containing genomes/contigs/scaffolds
-   -g = <string>: Gen(b)ank file(s) (gbk), comma separated list (default = None)
+   -g = <string>: Gen(b)ank file(s) (gbk), comma separated list for each replicon (default = None)
    -o = <string>: output directory? default [./P_CURRDATE_CURRTIME]
    -q = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)
    -r = <path>: (r)eference genome (set to ! to pick random one from genome dir)