Fixed inconsistent bwa_alg values

Used 'mem' in filter-sam.py, but 'bwamem' in extract-ref-alleles.py.
To remain consistent with 'aln', changed extract-ref-alleles.py to
'mem'.

Author: YourePrettyGood

extract-ref-alleles.py

@@ -334,7 +334,7 @@ def open_file(path):
                 #For SAM files generated from BWASW or STAMPY algorithms we don't get the same tags.  
                 #For now let reads through regardless of one best match or no suboptimal matches
                 ok = True
-            elif bwa_alg == 'bwamem':
+            elif bwa_alg == 'mem':
                 #SAM files generated by BWA-MEM do not get the same X* tags as produced by BWA-aln.
                 #We can use the AS and XS tags to check for repetitive mapping, and the CIGAR string
                 # to check for indels.