Allowed > 2^31 hits

[rsem.git] / wiggle.cpp

diff --git a/wiggle.cpp b/wiggle.cpp
index 19f52b480a00dcd991b30b583fce2ce0177a628b..c0cbdccc09ef8880b37ff5a01582d5e2869186f7 100644 (file)
--- a/wiggle.cpp
+++ b/wiggle.cpp
@@ -1,11 +1,13 @@
 #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"
 
 void add_bam_record_to_wiggle(const bam1_t *b, Wiggle& wiggle) {
@@ -36,29 +38,42 @@ void build_wiggles(const std::string& bam_filename,
                    WiggleProcessor& processor) {
     samfile_t *bam_in = samopen(bam_filename.c_str(), "rb", NULL);
        if (bam_in == 0) { fprintf(stderr, "Cannot open %s!\n", bam_filename.c_str()); exit(-1); }
-       //assert(bam_in != 0);
+
+       bam_header_t *header = bam_in->header;
+       bool *used = new bool[header->n_targets];
+       memset(used, 0, sizeof(bool) * header->n_targets);
 
     int cur_tid = -1; //current tid;
-       int cnt = 0;
+    HIT_INT_TYPE cnt;
     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) processor.process(wiggle);
+                       if (cur_tid >= 0) { used[cur_tid] = true; processor.process(wiggle); }
                        cur_tid = b->core.tid;
-            wiggle.name = bam_in->header->target_name[cur_tid];
-            wiggle.read_depth.assign(bam_in->header->target_len[cur_tid], 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);
                ++cnt;
-               if (cnt % 1000000 == 0) fprintf(stderr, "%d FIN\n", cnt);
+               if (cnt % 1000000 == 0) std::cout<< cnt<< std::endl;
        }
-       if (cur_tid >= 0) processor.process(wiggle);
+       if (cur_tid >= 0) { used[cur_tid] = true; processor.process(wiggle); }
+
+       for (int32_t i = 0; i < header->n_targets; i++)
+               if (!used[i]) {
+                       wiggle.name = header->target_name[i];
+                       wiggle.length = header->target_len[i];
+                       wiggle.read_depth.clear();
+                       processor.process(wiggle);
+               }
 
        samclose(bam_in);
        bam_destroy1(b);
+       delete[] used;
 }
 
 UCSCWiggleTrackWriter::UCSCWiggleTrackWriter(const std::string& output_filename,
@@ -75,9 +90,11 @@ UCSCWiggleTrackWriter::~UCSCWiggleTrackWriter() {
 
 void UCSCWiggleTrackWriter::process(const Wiggle& wiggle) {
     int sp, ep;
+
+    if (wiggle.read_depth.empty()) return;
     
     sp = ep = -1;
-    for (size_t i = 0; i < wiggle.read_depth.size(); i++) {
+    for (size_t i = 0; i < wiggle.length; i++) {
         if (wiggle.read_depth[i] > 0) {
             ep = i;
         }
@@ -102,9 +119,13 @@ ReadDepthWriter::ReadDepthWriter(std::ostream& stream)
 }
 
 void ReadDepthWriter::process(const Wiggle& wiggle) {
+
     stream_ << wiggle.name << '\t'
-            << wiggle.read_depth.size() << '\t';
-    for (size_t i = 0; i < wiggle.read_depth.size(); ++i) {
+            << wiggle.length << '\t';
+
+    if (wiggle.read_depth.empty()) { stream_ << "NA\n"; return; }
+
+    for (size_t i = 0; i < wiggle.length; ++i) {
         if (i > 0) stream_ << ' ';
         stream_ << wiggle.read_depth[i];
     }