Fixed index OOB error. Possible fix for remote X-forwarding

kcleal · Jan 15, 2024 · 482e2cc · 482e2cc
1 parent 959fb61
commit 482e2cc
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Showing 3 changed files with 23 additions and 7 deletions.
diff --git a/Makefile b/Makefile
@@ -126,7 +126,9 @@ OBJECTS = $(patsubst %.cpp, %.o, $(wildcard ./src/*.cpp))
 OBJECTS += $(patsubst %.c, %.o, $(wildcard ./lib/libBigWig/*.c))
 
 
-debug: LDFLAGS+=-fsanitize=address -fsanitize=undefined
+debug:
+    CXXFLAGS+=-g
+    LDFLAGS+=-fsanitize=address -fsanitize=undefined
 
 $(TARGET): $(OBJECTS)
 	$(CXX) -g $(OBJECTS) $(LDFLAGS) $(LDLIBS) -o $@

diff --git a/src/plot_manager.cpp b/src/plot_manager.cpp
@@ -185,8 +185,9 @@ namespace Manager {
 //        glfwWindowHint(GLFW_CONTEXT_VERSION_MAJOR, 3);
 //        glfwWindowHint(GLFW_CONTEXT_VERSION_MINOR, 2);
 //        glfwWindowHint(GLFW_OPENGL_DEBUG_CONTEXT, GLFW_TRUE);
-
-
+#ifndef __APPLE__
+        glfwWindowHint(GLFW_CONTEXT_CREATION_API , GLFW_EGL_CONTEXT_API);
+#endif
         window = glfwCreateWindow(width, height, "GW", NULL, NULL);
 
         if (!window) {

diff --git a/src/segments.cpp b/src/segments.cpp
@@ -572,34 +572,44 @@ namespace Segs {
     void findMismatches(const Themes::IniOptions &opts, ReadCollection &collection) {
 
         std::vector<Segs::Mismatches> &mm_array = collection.mmVector;
+        size_t mm_array_len = mm_array.size();
         const Utils::Region *region = collection.region;
+        if (region == nullptr) {
+            return;
+        }
         int regionLen = region->end - region->start;
         if (opts.max_coverage == 0 || regionLen > opts.snp_threshold) {
             return;
         }
+
         const char *refSeq = region->refSeq;
         if (refSeq == nullptr) {
             return;
         }
         for (const auto &align: collection.readQueue) {
-            if (align.y != -1) {
+            if (align.y != -1 || align.delegate == nullptr) {
                 continue;
             }
             uint32_t r_pos = align.pos;
             uint32_t cigar_l = align.delegate->core.n_cigar;
             uint8_t *ptr_seq = bam_get_seq(align.delegate);
             uint32_t *cigar_p = bam_get_cigar(align.delegate);
+            if (cigar_l == 0 || ptr_seq == nullptr || cigar_p == nullptr) {
+                continue;
+            }
             int r_idx;
             uint32_t idx = 0;
-
+            uint32_t qseq_len = align.delegate->core.l_qseq;
             uint32_t rlen = region->end - region->start;
             auto rbegin = (uint32_t) region->start;
             auto rend = (uint32_t) region->end;
             uint32_t op, l;
             for (uint32_t k = 0; k < cigar_l; k++) {
                 op = cigar_p[k] & BAM_CIGAR_MASK;
                 l = cigar_p[k] >> BAM_CIGAR_SHIFT;
-
+                if (idx >= qseq_len) {  // shouldn't happen
+                    break;
+                }
                 switch (op) {
                     case BAM_CSOFT_CLIP:
                     case BAM_CINS:
@@ -617,7 +627,7 @@ namespace Segs {
                         break;
                     case BAM_CDIFF:
                         for (uint32_t i = 0; i < l; ++i) {
-                            if (r_pos >= rbegin && r_pos < rend) {
+                            if (r_pos >= rbegin && r_pos < rend && r_pos - rbegin < mm_array_len) {
                                 char bam_base = bam_seqi(ptr_seq, idx);
                                 switch (bam_base) {
                                     case 1:
@@ -652,6 +662,9 @@ namespace Segs {
                             if (r_idx >= (int)rlen) {
                                 break;
                             }
+                            if (r_pos - rbegin >= mm_array_len) {
+                                break;
+                            }
 
                             char ref_base;
                             switch (refSeq[r_idx]) {