From 7c1a6a58e16e0f49eb95b37e3cbab369357d6414 Mon Sep 17 00:00:00 2001
From: Sina Booeshaghi <sbooeshaghi@gmail.com>
Date: Wed, 7 Aug 2024 15:07:22 -0700
Subject: [PATCH] update the spec to enable zero length regions and zero length
 sequences when min_len is zero

---
 seqspec/Region.py                  |  4 ++--
 seqspec/schema/seqspec.schema.json | 29 ++++++++++++++++++++++++++---
 2 files changed, 28 insertions(+), 5 deletions(-)

diff --git a/seqspec/Region.py b/seqspec/Region.py
index 4845bd6..1e64a73 100644
--- a/seqspec/Region.py
+++ b/seqspec/Region.py
@@ -75,9 +75,9 @@ def update_attr(self):
         self.sequence = self.get_sequence()
         self.min_len, self.max_len = self.get_len()
         if self.sequence_type == "random":
-            self.sequence = "X" * self.max_len
+            self.sequence = "X" * self.min_len
         if self.sequence_type == "onlist":
-            self.sequence = "N" * self.max_len
+            self.sequence = "N" * self.min_len
         return
 
     def __repr__(self) -> str:
diff --git a/seqspec/schema/seqspec.schema.json b/seqspec/schema/seqspec.schema.json
index 3c23f20..2644251 100644
--- a/seqspec/schema/seqspec.schema.json
+++ b/seqspec/schema/seqspec.schema.json
@@ -144,8 +144,7 @@
         },
         "sequence": {
           "description": "The sequence",
-          "type": "string",
-          "pattern": "^[ACGTRYMKSWHBVDNX]+$"
+          "type": "string"
         },
         "min_len": {
           "description": "The minimum length of the sequence",
@@ -194,7 +193,31 @@
         "sequence",
         "min_len",
         "max_len"
-      ]
+      ],
+      "if": {
+        "properties": {
+          "min_len": {
+            "const": 0
+          }
+        }
+      },
+      "then": {
+        "properties": {
+          "sequence": {
+            "type": "string",
+            "pattern": "^[ACGTRYMKSWHBVDNX]*$"
+          }
+        }
+      },
+      "else": {
+        "properties": {
+          "sequence": {
+            "type": "string",
+            "minLength": 1,
+            "pattern": "^[ACGTRYMKSWHBVDNX]+$"
+          }
+        }
+      }
     },
     "read": {
       "title": "Read",