Refactored wiggle code and added rsem-bam2readdepth program

[rsem.git] / bam2wig.cpp

diff --git a/bam2wig.cpp b/bam2wig.cpp
index fcb86b3c562373a0a0492a4de875e6565c551b94..cb02bc2a9a6f575235dfe13bf9b581aca0852a12 100644 (file)
--- a/bam2wig.cpp
+++ b/bam2wig.cpp
@@ -1,103 +1,15 @@
-#include<cstdio>
-#include<cstring>
-#include<cstdlib>
-#include<cassert>
-#include<string>
-
-#include "sam/bam.h"
-#include "sam/sam.h"
+#include <cstdio>
+#include "wiggle.h"
 
 using namespace std;
 
-samfile_t *bam_in;
-bam1_t *b;
-
-int cur_tid; //current tid;
-float *wig_arr; // wiggle array
-FILE *fo;
-
-void generateWiggle(int tid) {
-       int chr_len = bam_in->header->target_len[tid];
-       char *chr_name = bam_in->header->target_name[tid];
-       int sp, ep;
-
-       sp = ep = -1;
-       for (int i = 0; i < chr_len; i++) {
-               if (wig_arr[i] > 0) {
-                       ep = i;
-               }
-               else {
-                       if (sp < ep) {
-                               ++sp;
-                               fprintf(fo, "fixedStep chrom=%s start=%d step=1\n", chr_name, sp + 1);
-                               for (int j = sp; j <= ep; j++) fprintf(fo, "%.7g\n", wig_arr[j]);
-                       }
-                       sp = i;
-               }
-       }
-       if (sp < ep) {
-               ++sp;
-               fprintf(fo, "fixedStep chrom=%s start=%d step=1\n", chr_name, sp + 1);
-               for (int j = sp; j <= ep; j++) fprintf(fo, "%.7g\n", wig_arr[j]);
-       }
-}
-
 int main(int argc, char* argv[]) {
-       int cnt = 0;
-
        if (argc != 4) {
-               printf("Usage : rsem-bam2wig sorted_bam_input wig_output wiggle_name\n");
+               printf("Usage: rsem-bam2wig sorted_bam_input wig_output wiggle_name\n");
                exit(-1);
        }
-
-       bam_in = samopen(argv[1], "rb", NULL);
-       if (bam_in == 0) { fprintf(stderr, "Cannot open %s!\n", argv[1]); exit(-1); }
-       //assert(bam_in != 0);
-       b = bam_init1();
-
-       fo = fopen(argv[2], "w");
-       fprintf(fo, "track type=wiggle_0 name=\"%s\" description=\"%s\" visibility=full\n", argv[3], argv[3]);
-
-       cur_tid = -1;
-       wig_arr = NULL;
-       while (samread(bam_in, b) >= 0) {
-               if (b->core.tid != cur_tid) {
-                       if (cur_tid >= 0) generateWiggle(cur_tid);
-                       cur_tid = b->core.tid;
-                       size_t len = sizeof(float) * bam_in->header->target_len[cur_tid];
-                       wig_arr = (float*)realloc(wig_arr, len);
-                       memset(wig_arr, 0, len);
-               }
-
-               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) wig_arr[pos] += w;
-                               break;
-                       case BAM_CREF_SKIP : pos += op_len; break;
-                       default : assert(false);
-                       }
-               }
-
-               ++cnt;
-               if (cnt % 1000000 == 0) printf("%d FIN\n", cnt);
-       }
-       if (cur_tid >= 0) generateWiggle(cur_tid);
-       free(wig_arr);
-
-       samclose(bam_in);
-       bam_destroy1(b);
-
-       fclose(fo);
+    UCSCWiggleTrackWriter track_writer(argv[2], argv[3]);
+    build_wiggles(argv[1], track_writer);
 
        return 0;
 }