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); +} +