Added error detection for cases such as a read's two mates having different names...

[rsem.git] / wiggle.cpp

diff --git a/wiggle.cpp b/wiggle.cpp
index c0cbdccc09ef8880b37ff5a01582d5e2869186f7..00dcce8d431edc2c38c0891d17b8085dbcbac25b 100644 (file)
--- a/wiggle.cpp
+++ b/wiggle.cpp
@@ -10,9 +10,18 @@
 #include "utils.h"
 #include "wiggle.h"
 
+bool no_fractional_weight = false;
+
 void add_bam_record_to_wiggle(const bam1_t *b, Wiggle& wiggle) {
-    uint8_t *p_tag = bam_aux_get(b, "ZW");
-    float w = (p_tag != NULL ? bam_aux2f(p_tag) : 1.0);
+    double w;
+
+    if (no_fractional_weight) w = 1.0;
+    else {
+      uint8_t *p_tag = bam_aux_get(b, "ZW");
+      if (p_tag == NULL) return;
+      w = bam_aux2f(p_tag);
+    }
+
     int pos = b->core.pos;
     uint32_t *p = bam1_cigar(b);
     
@@ -43,21 +52,21 @@ void build_wiggles(const std::string& bam_filename,
        bool *used = new bool[header->n_targets];
        memset(used, 0, sizeof(bool) * header->n_targets);
 
-    int cur_tid = -1; //current tid;
-    HIT_INT_TYPE cnt;
-    bam1_t *b = bam_init1();
-    Wiggle wiggle;
+       int cur_tid = -1; //current tid;
+       HIT_INT_TYPE cnt = 0;
+       bam1_t *b = bam_init1();
+       Wiggle wiggle;
        while (samread(bam_in, b) >= 0) {
                if (b->core.flag & 0x0004) continue;
 
                if (b->core.tid != cur_tid) {
                        if (cur_tid >= 0) { used[cur_tid] = true; processor.process(wiggle); }
                        cur_tid = b->core.tid;
-            wiggle.name = header->target_name[cur_tid];
-            wiggle.length = header->target_len[cur_tid];
-            wiggle.read_depth.assign(wiggle.length, 0.0);
+                       wiggle.name = header->target_name[cur_tid];
+                       wiggle.length = header->target_len[cur_tid];
+                       wiggle.read_depth.assign(wiggle.length, 0.0);
                }
-        add_bam_record_to_wiggle(b, wiggle);
+               add_bam_record_to_wiggle(b, wiggle);
                ++cnt;
                if (cnt % 1000000 == 0) std::cout<< cnt<< std::endl;
        }
@@ -95,14 +104,14 @@ void UCSCWiggleTrackWriter::process(const Wiggle& wiggle) {
     
     sp = ep = -1;
     for (size_t i = 0; i < wiggle.length; i++) {
-        if (wiggle.read_depth[i] > 0) {
+        if (wiggle.read_depth[i] >= 0.0095) {
             ep = i;
         }
         else {
             if (sp < ep) {
                 ++sp;
                 fprintf(fo, "fixedStep chrom=%s start=%d step=1\n", wiggle.name.c_str(), sp + 1);
-                for (int j = sp; j <= ep; j++) fprintf(fo, "%.7g\n", wiggle.read_depth[j]);
+                for (int j = sp; j <= ep; j++) fprintf(fo, "%.2f\n", wiggle.read_depth[j]);
             }
             sp = i;
         }
@@ -110,7 +119,7 @@ void UCSCWiggleTrackWriter::process(const Wiggle& wiggle) {
     if (sp < ep) {
         ++sp;
         fprintf(fo, "fixedStep chrom=%s start=%d step=1\n", wiggle.name.c_str(), sp + 1);
-        for (int j = sp; j <= ep; j++) fprintf(fo, "%.7g\n", wiggle.read_depth[j]);
+        for (int j = sp; j <= ep; j++) fprintf(fo, "%.2f\n", wiggle.read_depth[j]);
     }
 }