diff --git a/iGDA.xcodeproj/project.xcworkspace/xcuserdata/zhixingfeng.xcuserdatad/UserInterfaceState.xcuserstate b/iGDA.xcodeproj/project.xcworkspace/xcuserdata/zhixingfeng.xcuserdatad/UserInterfaceState.xcuserstate
index cfccdce0..f72784fd 100644
Binary files a/iGDA.xcodeproj/project.xcworkspace/xcuserdata/zhixingfeng.xcuserdatad/UserInterfaceState.xcuserstate and b/iGDA.xcodeproj/project.xcworkspace/xcuserdata/zhixingfeng.xcuserdatad/UserInterfaceState.xcuserstate differ
diff --git a/iGDA.xcodeproj/xcuserdata/zhixingfeng.xcuserdatad/xcdebugger/Breakpoints_v2.xcbkptlist b/iGDA.xcodeproj/xcuserdata/zhixingfeng.xcuserdatad/xcdebugger/Breakpoints_v2.xcbkptlist
index f929b416..7cf16e85 100644
--- a/iGDA.xcodeproj/xcuserdata/zhixingfeng.xcuserdatad/xcdebugger/Breakpoints_v2.xcbkptlist
+++ b/iGDA.xcodeproj/xcuserdata/zhixingfeng.xcuserdatad/xcdebugger/Breakpoints_v2.xcbkptlist
@@ -12,12 +12,12 @@
ignoreCount = "0"
continueAfterRunningActions = "No"
filePath = "src/modules/assemble/assembler.cpp"
- timestampString = "590545323.447065"
+ timestampString = "603425340.151193"
startingColumnNumber = "9223372036854775807"
endingColumnNumber = "9223372036854775807"
startingLineNumber = "760"
endingLineNumber = "760"
- landmarkName = "Assembler::ann_clust_recode(recode_file, recode_ref_file, encode_file, align_file, var_file, min_cvg, min_prop, max_prop, topn, max_nn, min_jaccard, is_correct, is_hang, max_iter, is_recode)"
+ landmarkName = "Assembler::ann_clust_recode(string recode_file, string recode_ref_file, string encode_file, string align_file, string var_file, int min_cvg, double min_prop, double max_prop, int topn, int max_nn, double min_jaccard, bool is_correct, bool is_hang, int max_iter, bool is_recode)"
landmarkType = "7">
@@ -29,12 +29,12 @@
ignoreCount = "0"
continueAfterRunningActions = "No"
filePath = "src/modules/assemble/assembler.cpp"
- timestampString = "590545323.44719"
+ timestampString = "603425340.152985"
startingColumnNumber = "9223372036854775807"
endingColumnNumber = "9223372036854775807"
startingLineNumber = "774"
endingLineNumber = "774"
- landmarkName = "Assembler::ann_clust_recode(recode_file, recode_ref_file, encode_file, align_file, var_file, min_cvg, min_prop, max_prop, topn, max_nn, min_jaccard, is_correct, is_hang, max_iter, is_recode)"
+ landmarkName = "Assembler::ann_clust_recode(string recode_file, string recode_ref_file, string encode_file, string align_file, string var_file, int min_cvg, double min_prop, double max_prop, int topn, int max_nn, double min_jaccard, bool is_correct, bool is_hang, int max_iter, bool is_recode)"
landmarkType = "7">
@@ -46,12 +46,12 @@
ignoreCount = "0"
continueAfterRunningActions = "No"
filePath = "src/modules/assemble/assembler.cpp"
- timestampString = "590545323.44726"
+ timestampString = "603425340.153415"
startingColumnNumber = "9223372036854775807"
endingColumnNumber = "9223372036854775807"
startingLineNumber = "781"
endingLineNumber = "781"
- landmarkName = "Assembler::ann_clust_recode(recode_file, recode_ref_file, encode_file, align_file, var_file, min_cvg, min_prop, max_prop, topn, max_nn, min_jaccard, is_correct, is_hang, max_iter, is_recode)"
+ landmarkName = "Assembler::ann_clust_recode(string recode_file, string recode_ref_file, string encode_file, string align_file, string var_file, int min_cvg, double min_prop, double max_prop, int topn, int max_nn, double min_jaccard, bool is_correct, bool is_hang, int max_iter, bool is_recode)"
landmarkType = "7">
@@ -63,12 +63,12 @@
ignoreCount = "0"
continueAfterRunningActions = "No"
filePath = "src/modules/assemble/assembler.cpp"
- timestampString = "590545323.44732"
+ timestampString = "603425340.153754"
startingColumnNumber = "9223372036854775807"
endingColumnNumber = "9223372036854775807"
startingLineNumber = "783"
endingLineNumber = "783"
- landmarkName = "Assembler::ann_clust_recode(recode_file, recode_ref_file, encode_file, align_file, var_file, min_cvg, min_prop, max_prop, topn, max_nn, min_jaccard, is_correct, is_hang, max_iter, is_recode)"
+ landmarkName = "Assembler::ann_clust_recode(string recode_file, string recode_ref_file, string encode_file, string align_file, string var_file, int min_cvg, double min_prop, double max_prop, int topn, int max_nn, double min_jaccard, bool is_correct, bool is_hang, int max_iter, bool is_recode)"
landmarkType = "7">
@@ -127,7 +127,7 @@
BreakpointExtensionID = "Xcode.Breakpoint.FileBreakpoint">
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/src/modules/assemble/assembler.cpp b/src/modules/assemble/assembler.cpp
index 1124fc25..b18d654a 100644
--- a/src/modules/assemble/assembler.cpp
+++ b/src/modules/assemble/assembler.cpp
@@ -1207,7 +1207,7 @@ void Assembler::ann_to_graph(Graph &gp, string ann_file, double min_prop, double
for (int64_t j = 0; j < this->rl_ann_clust.size(); ++j){
if (j == i) continue;
- if (rl_ann_clust[j].start < rl_ann_clust[i].start || rl_ann_clust[j].start >= rl_ann_clust[i].end || rl_ann_clust[j].end <= rl_ann_clust[i].end)
+ if (rl_ann_clust[j].start < rl_ann_clust[i].start || rl_ann_clust[j].start >= rl_ann_clust[i].end || rl_ann_clust[j].end < rl_ann_clust[i].end)
continue;
int overlap_len = rl_ann_clust[i].end - rl_ann_clust[j].start + 1;
diff --git a/test/test_assembler.cpp b/test/test_assembler.cpp
index 1cf87d91..9d1516ea 100644
--- a/test/test_assembler.cpp
+++ b/test/test_assembler.cpp
@@ -558,3 +558,15 @@ TEST_CASE("test dforest in polish()", "[hide]")
forestsnvstxxl.run(encode_file, m5_file, cmpreads_file, out_file, tmp_dir, 10, 1000, 1, 0.3, 1, 1, true);
}
+
+TEST_CASE("debug Assemble::ann_to_graph()", "[hide]")
+{
+ string ann_file = "/Users/zhixingfeng/Dropbox/work/iGDA/development/test/test_polish/phase/clpX_1/realign.ann.tested.ft.count.ft";
+ Assembler assembler;
+ Graph gp;
+ assembler.ann_to_graph(gp, ann_file);
+
+ ofstream fs_graph(ann_file + ".dot");
+ boost::write_graphviz(fs_graph, gp);
+}
+