Merge branch 'flt-p' into dev-lh3

Overlaps.cpp

@@ -22279,7 +22279,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
 
 
     
-    enable_debug_mode(1);
+    ///enable_debug_mode(1);
 
     purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
     min_ovlp, bubble_dist, drop_ratio, 0);
@@ -22301,7 +22301,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
     ///debug_purge_dup = 1;
     ///deduplicate_advance(*ug, read_g, coverage_cut, sources, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, 0);
     ///delete_useless_nodes(ug);
-    enable_debug_mode(0);
+    ///enable_debug_mode(0);
     purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
     min_ovlp, bubble_dist, drop_ratio, 0);
     delete_useless_nodes(ug);

Overlaps.h

@@ -365,11 +365,21 @@ typedef struct {
 	uint32_t pre_n_seq, seqID; 
 } C_graph;
 
+typedef struct {
+	kvec_t(uint8_t) a;
+	uint32_t i;
+} kvec_t_u8_warp;
+
 typedef struct {
 	kvec_t(uint32_t) a;
 	uint32_t i;
 } kvec_t_u32_warp;
 
+typedef struct {
+	kvec_t(int32_t) a;
+	uint32_t i;
+} kvec_t_i32_warp;
+
 typedef struct {
 	kvec_t(uint64_t) a;
 	uint64_t i;