Refactored wiggle code and added rsem-bam2readdepth program

[rsem.git] / wiggle.cpp

diff --git a/wiggle.cpp b/wiggle.cpp
new file mode 100644 (file)
index 0000000..90b6f8b
--- /dev/null
+++ b/wiggle.cpp
@@ -0,0 +1,108 @@
+#include <cstring>
+#include <cstdlib>
+#include <cassert>
+
+#include "wiggle.h"
+
+#include "sam/bam.h"
+#include "sam/sam.h"
+
+void add_bam_record_to_wiggle(const bam1_t *b, Wiggle& wiggle) {
+    float w = bam_aux2f(bam_aux_get(b, "ZW"));
+    int pos = b->core.pos;
+    uint32_t *p = bam1_cigar(b);
+    
+    for (int i = 0; i < (int)b->core.n_cigar; i++, ++p) {
+        int op = *p & BAM_CIGAR_MASK;
+        int op_len = *p >> BAM_CIGAR_SHIFT;
+        
+        switch (op) {
+            //case BAM_CSOFT_CLIP : pos += op_len; break;
+        case BAM_CINS : pos += op_len; break;
+        case BAM_CMATCH :
+            for (int j = 0; j < op_len; j++, ++pos) {
+                wiggle.read_depth[pos] += w;
+            }
+            break;
+        case BAM_CREF_SKIP : pos += op_len; break;
+        default : assert(false);
+        }
+    }
+}
+
+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);
+
+    int cur_tid = -1; //current tid;
+       int cnt = 0;
+    bam1_t *b = bam_init1();
+    Wiggle wiggle;
+       while (samread(bam_in, b) >= 0) {
+               if (b->core.tid != cur_tid) {
+                       if (cur_tid >= 0) 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);
+               }
+        add_bam_record_to_wiggle(b, wiggle);
+               ++cnt;
+               if (cnt % 1000000 == 0) fprintf(stderr, "%d FIN\n", cnt);
+       }
+       if (cur_tid >= 0) processor.process(wiggle);
+
+       samclose(bam_in);
+       bam_destroy1(b);
+}
+
+UCSCWiggleTrackWriter::UCSCWiggleTrackWriter(const std::string& output_filename,
+                                             const std::string& track_name) {
+    fo = fopen(output_filename.c_str(), "w");
+    fprintf(fo, "track type=wiggle_0 name=\"%s\" description=\"%s\" visibility=full\n",
+            track_name.c_str(),
+            track_name.c_str());
+}
+
+UCSCWiggleTrackWriter::~UCSCWiggleTrackWriter() {
+    fclose(fo);
+}
+
+void UCSCWiggleTrackWriter::process(const Wiggle& wiggle) {
+    int sp, ep;
+    
+    sp = ep = -1;
+    for (size_t i = 0; i < wiggle.read_depth.size(); i++) {
+        if (wiggle.read_depth[i] > 0) {
+            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]);
+            }
+            sp = i;
+        }
+    }
+    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]);
+    }
+}
+
+ReadDepthWriter::ReadDepthWriter(std::ostream& stream) 
+    : stream_(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) {
+        if (i > 0) stream_ << ' ';
+        stream_ << wiggle.read_depth[i];
+    }
+    stream_ << '\n';
+}