* samtools-0.1.5-8 (r404)

[samtools.git] / sam.c

diff --git a/sam.c b/sam.c
index 4c16b02fb87de19426f50dc3e1573b3f58801a26..45cb05cf3dd6f8a04acfd4dd92c8d250835855a2 100644 (file)
--- a/sam.c
+++ b/sam.c
@@ -22,6 +22,18 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
        if (h0->rg2lib) h->rg2lib = bam_strmap_dup(h0->rg2lib);
        return h;
 }
+static void append_header_text(bam_header_t *header, char* text, int len)
+{
+       int x = header->l_text + 1;
+       int y = header->l_text + len + 1; // 1 byte null
+       if (text == 0) return;
+       kroundup32(x); 
+       kroundup32(y);
+       if (x < y) header->text = (char*)realloc(header->text, y);
+       strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
+       header->l_text += len;
+       header->text[header->l_text] = 0;
+}
 
 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 {
@@ -40,8 +52,10 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
                        fp->header = sam_header_read(fp->x.tamr);
                        if (fp->header->n_targets == 0) { // no @SQ fields
                                if (aux) { // check if aux is present
-                                       bam_header_destroy(fp->header);
+                                       bam_header_t *textheader = fp->header;
                                        fp->header = sam_header_read2((const char*)aux);
+                                       append_header_text(fp->header, textheader->text, textheader->l_text);
+                                       bam_header_destroy(textheader);
                                }
                                if (fp->header->n_targets == 0)
                                        fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
@@ -120,7 +134,7 @@ int samwrite(samfile_t *fp, const bam1_t *b)
        }
 }
 
-int sampileup(samfile_t *fp, int mask, int min_mapQ, bam_pileup_f func, void *func_data)
+int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
 {
        bam_plbuf_t *buf;
        int ret;
@@ -129,8 +143,7 @@ int sampileup(samfile_t *fp, int mask, int min_mapQ, bam_pileup_f func, void *fu
        buf = bam_plbuf_init(func, func_data);
        bam_plbuf_set_mask(buf, mask);
        while ((ret = samread(fp, b)) >= 0)
-               if (b->core.qual >= min_mapQ)
-                       bam_plbuf_push(b, buf);
+               bam_plbuf_push(b, buf);
        bam_plbuf_push(0, buf);
        bam_plbuf_destroy(buf);
        bam_destroy1(b);