X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=wiggle.cpp;h=00dcce8d431edc2c38c0891d17b8085dbcbac25b;hp=65a3d4a783e1ffd44e3b534c890113138aff8aee;hb=HEAD;hpb=5fd66ada6c610981dcecd50e5e41436e0458b110

diff --git a/wiggle.cpp b/wiggle.cpp
index 65a3d4a..00dcce8 100644
--- a/wiggle.cpp
+++ b/wiggle.cpp
@@ -1,16 +1,27 @@
 #include <cstring>
 #include <cstdlib>
 #include <cassert>
+#include <iostream>
 
 #include <stdint.h>
 #include "sam/bam.h"
 #include "sam/sam.h"
 
+#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);
     
@@ -41,23 +52,23 @@ 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;
-	int cnt = 0;
-    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) fprintf(stderr, "%d FIN\n", cnt);
+		if (cnt % 1000000 == 0) std::cout<< cnt<< std::endl;
 	}
 	if (cur_tid >= 0) { used[cur_tid] = true; processor.process(wiggle); }
 
@@ -93,14 +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;
         }
@@ -108,7 +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]);
     }
 }