rsem v1.1.14, add --sampling-for-bam option, modify rsem-bam2wig to handle BAM files...

[rsem.git] / bam2wig.cpp

diff --git a/bam2wig.cpp b/bam2wig.cpp
index fcb86b3c562373a0a0492a4de875e6565c551b94..e46fa67bc3812c8ca6978aeb8c6764680c3549b9 100644 (file)
--- a/bam2wig.cpp
+++ b/bam2wig.cpp
@@ -4,6 +4,8 @@
 #include<cassert>
 #include<string>
 
+#include<stdint.h>
+
 #include "sam/bam.h"
 #include "sam/sam.h"
 
@@ -61,6 +63,8 @@ int main(int argc, char* argv[]) {
        cur_tid = -1;
        wig_arr = NULL;
        while (samread(bam_in, b) >= 0) {
+               if (b->core.flag & 0x0004) continue;
+               
                if (b->core.tid != cur_tid) {
                        if (cur_tid >= 0) generateWiggle(cur_tid);
                        cur_tid = b->core.tid;
@@ -69,7 +73,8 @@ int main(int argc, char* argv[]) {
                        memset(wig_arr, 0, len);
                }
 
-               float w = bam_aux2f(bam_aux_get(b, "ZW"));
+               uint8_t *p_tag = bam_aux_get(b, "ZW");
+               float w = (p_tag != NULL ? bam_aux2f(p_tag) : 1.0);
                int pos = b->core.pos;
                uint32_t *p = bam1_cigar(b);