On branch temp

pyloh/preprocess/io.py: raise error if the ref feeded from command line is different from the bam files
uci-cbcl · Jan 10, 2014 · 12ada45 · 12ada45
1 parent 1dfa9af
commit 12ada45
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/pyloh/preprocess/io.py b/pyloh/preprocess/io.py
@@ -45,6 +45,11 @@ def next(self):
             pos = normal_column.pos
             ref_base = self.ref_genome_fasta.fetch(self.chrom, pos, pos + 1).upper()
 
+            if ref_base == '':
+                print 'Error: %s does not match the reference of the bam files' \
+                % self.ref_genome_fasta.filename
+                sys.exit(-1)
+
             paired_counts = self._get_paired_counts(normal_column, tumor_column, pos, ref_base)
 
             if paired_counts == None: