Fix to sam2interval bug reported by Kathy So. The bug was causing sam2interval to successfully parse unmapped sam entries, which have no valid coordinate.

tools/samtools/sam2interval.py

@@ -93,10 +93,12 @@ options (listed below) default to 'None' if omitted
             read_name = fields[ int( options.read_col ) - 1 ]
             ref_name  = fields[ int( options.ref_col ) - 1 ]
             
-            if options.prt_all:
-                print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, line)
-            else:
-                print '%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand)
+	    if not ref_name == '*':
+	    # Do not print lines with unmapped reads that contain '*' instead of chromosome name	    
+		if options.prt_all:	
+		    print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, line)
+		else:
+		    print '%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand)
 
 if __name__ == "__main__": main()
 

tools/samtools/sam2interval.xml

@@ -23,6 +23,11 @@
         <param name="print_all" value="No"/>
         <output name="out_file1" file="sam2interval_noprintAll.dat" ftype="interval"/>
     </test>
+    <test>
+        <param name="input1" value="sam2interval-test3.sam" ftype="sam"/>
+        <param name="print_all" value="No"/>
+        <output name="out_file1" file="sam2interval_with_unmapped_reads_noprintAll.dat" ftype="interval"/>
+    </test>
 
 </tests>
   <help>