Computes CIGAR code for seeds, and extends seeds first to the left-side, and then ,to the right-side (for an efficient CIGAR generatiion)

Author: jtarraga

.gitignore

@@ -6,6 +6,8 @@
 *.gch
 *~
 
+*.OLD
+
 # Build folders
 bin/*
 build/*

src/dna/dna_aligner.c

@@ -1,6 +1,11 @@
 #include "dna_aligner.h"
 //--------------------------------------------------------------------
 
+#ifdef _VERBOSE
+extern int num_dup_reads;
+extern int num_total_dup_reads;
+#endif
+
 //--------------------------------------------------------------------
 // main 
 //--------------------------------------------------------------------