From 30d451126bf1f484b343f98066ff89a03098b7f1 Mon Sep 17 00:00:00 2001
From: mnshgl0110 <mnshgl0110.gmail.com>
Date: Wed, 11 Dec 2024 16:00:04 +0100
Subject: [PATCH] Catch exception when there are no short variations between
 the genomes.

---
 syri/__init__.py          |  2 +-
 syri/pyxFiles/findshv.pyx | 12 ++++++++++--
 syri/pyxFiles/findsv.pyx  |  3 +--
 3 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/syri/__init__.py b/syri/__init__.py
index 16c83d8..83b020e 100644
--- a/syri/__init__.py
+++ b/syri/__init__.py
@@ -1 +1 @@
-__version__ = "1.7.0"
\ No newline at end of file
+__version__ = "1.7.1"
\ No newline at end of file
diff --git a/syri/pyxFiles/findshv.pyx b/syri/pyxFiles/findshv.pyx
index 98ad88a..40c6a59 100644
--- a/syri/pyxFiles/findshv.pyx
+++ b/syri/pyxFiles/findshv.pyx
@@ -190,8 +190,16 @@ def getshv(args, coords, chrlink):
             logger.error('Error in finding SNPs using show-snps: ' + out[1].decode())
             sys.exit()
         else:
-            allsnps = pd.read_table(cwdpath + prefix + fname, header = None)
-            logger.debug('finished writing SNPs')
+            try:
+                allsnps = pd.read_table(cwdpath + prefix + fname, header = None)
+                logger.debug('finished writing SNPs')
+            except pd.errors.EmptyDataError as e:
+                logger.warning('No SNPs or small indels were identified in the alignments.')
+                if mapit == 1:
+                    fileRemove(cwdpath + prefix + fname)
+                with open(cwdpath + prefix + 'snps.txt', "w") as fout:
+                    pass
+                return None
 
         achrs = pd.unique(allAlignments['aChr'])
         bchrs = pd.unique(allAlignments['bChr'])
diff --git a/syri/pyxFiles/findsv.pyx b/syri/pyxFiles/findsv.pyx
index 942bcc2..2a01f1e 100644
--- a/syri/pyxFiles/findsv.pyx
+++ b/syri/pyxFiles/findsv.pyx
@@ -109,8 +109,7 @@ def getSV(cwdPath, allAlignments, prefix, offset):
     logger = logging.getLogger("getSV")
     offset = -abs(offset)
     fout = open(cwdPath + prefix + "sv.txt", "w")
-    allAlignments["id"] = allAlignments.group.astype(
-        "str") + 'Chr' + allAlignments.aChr + 'Chr' + allAlignments.bChr + allAlignments.state
+    allAlignments["id"] = allAlignments.group.astype("str") + 'Chr' + allAlignments.aChr + 'Chr' + allAlignments.bChr + allAlignments.state
     allBlocks = pd.unique(allAlignments.id)
 
     for i in allBlocks: