#531 - fixed reference reading

Author: Hermann Romanek

src/sniffles/result.py

@@ -171,6 +171,7 @@ def store_calls(self, svcalls):
 
         with open(self.tmpfile_name, 'a') as f:
             vcf = VCF(SnifflesConfig.GLOBAL, f)
+            vcf.open_reference(generate_index=False)
             for call in svcalls[offset:]:
                 vcf.write_call(call)
 

src/sniffles/vcf.py

@@ -98,15 +98,18 @@ def __init__(self, config: SnifflesConfig, handle):
         self.reference_handle = None
         self.header_str = ""
 
-    def open_reference(self):
+    def open_reference(self, generate_index: bool = True):
         if self.config.reference is None:
             return
 
-        if not os.path.exists(self.config.reference + ".fai") and not os.path.exists(self.config.reference + ".gzi"):
-            print(f"Info: Fasta index for {self.config.reference} not found. Generating with pysam.faidx "
-                  f"(this may take a while)")
+        if not os.path.exists(self.config.reference + ".fai") and not os.path.exists(self.config.reference + ".gzi") and generate_index:
+            log.warning(f"Fasta index for {self.config.reference} not found. Generating with pysam.faidx (this may take a while)")
             pysam.faidx(self.config.reference)
-        self.reference_handle = pysam.FastaFile(self.config.reference)
+
+        try:
+            self.reference_handle = pysam.FastaFile(self.config.reference)
+        except:
+            log.error(f'Unable to open reference file {self.config.reference}')
 
     def write_header(self, contigs_lengths):
         self.write_header_line("fileformat=VCFv4.2")