From 929bbbe5bce1368a104f88fcb7514ee0e1db7bee Mon Sep 17 00:00:00 2001
From: Kirill Bessonov <kbessonov@gmail.com>
Date: Tue, 1 Oct 2024 16:25:05 -0400
Subject: [PATCH] Updated README.md and CHANGELOG.md

---
 README.rst | 55 +++++++++++++++++++++++++++---------------------------
 1 file changed, 28 insertions(+), 27 deletions(-)

diff --git a/README.rst b/README.rst
index 53736d1..3ebc2df 100644
--- a/README.rst
+++ b/README.rst
@@ -293,12 +293,38 @@ Summary of output options:
 
 Primary results output (``-o sistr-results``)
 ---------------------------------------------
-SISTR supports various output formats specified by the ``-f`` with ``json`` being the default.
+SISTR supports various text output formats specified by the ``-f`` option with ``json`` being the default.
+
+JSON results output (``-f json``):
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. code-block:: json
+
+	[
+	  {
+	    "serovar_cgmlst": "Typhimurium",
+	    "cgmlst_matching_alleles": 327,
+	    "h1": "i",
+	    "serovar_antigen": "Typhimurium",
+	    "cgmlst_distance": 0.009090909090909038,
+	    "h2": "1,2",
+	    "cgmlst_genome_match": "LT2",
+	    "cgmlst_ST": 660408169,
+	    "serovar": "Typhimurium",
+	    "fasta_filepath": "/full/path/to/LT2.fasta",
+	    "genome": "LT2",
+	    "serogroup": "B",
+	    "qc_messages": "",
+	    "qc_status": "PASS",
+	    "o_antigen": "1,4,[5],12",
+	    "cgmlst_subspecies": "enterica"
+	  }
+	]
+
 
 Tab-delimited results output (``-f tab``):
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. code-block:: tab
+.. code-block:: text
 	
 	cgmlst_ST	cgmlst_distance	cgmlst_genome_match	cgmlst_matching_alleles	cgmlst_subspecies	fasta_filepath	genome	h1	h2	o_antigen	qc_messages	qc_status	serogroup	serovar	serovar_antigen	serovar_cgmlst
 	660408169	0.00909090909091	LT2	327	enterica	/home/peter/Downloads/sistr-LT2-example/LT2.fasta	LT2	i	1,2	1,4,[5],12		PASS	B	Typhimurium	Typhimurium	Typhimurium
@@ -320,31 +346,6 @@ The same ``csv`` results rendered as a table
 	660408169,0.00909090909091,LT2,327,enterica,/home/peter/Downloads/sistr-LT2-example/LT2.fasta,LT2,i,"1,2","1,4,[5],12",,PASS,B,Typhimurium,Typhimurium,Typhimurium
 
 
-JSON results output:
-~~~~~~~~~~~~~~~~~~~~
-.. code-block:: json
-
-	[
-	  {
-	    "serovar_cgmlst": "Typhimurium",
-	    "cgmlst_matching_alleles": 327,
-	    "h1": "i",
-	    "serovar_antigen": "Typhimurium",
-	    "cgmlst_distance": 0.009090909090909038,
-	    "h2": "1,2",
-	    "cgmlst_genome_match": "LT2",
-	    "cgmlst_ST": 660408169,
-	    "serovar": "Typhimurium",
-	    "fasta_filepath": "/full/path/to/LT2.fasta",
-	    "genome": "LT2",
-	    "serogroup": "B",
-	    "qc_messages": "",
-	    "qc_status": "PASS",
-	    "o_antigen": "1,4,[5],12",
-	    "cgmlst_subspecies": "enterica"
-	  }
-	]
-
 cgMLST allele search results
 -------------------------------------