X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.c;h=45cb05cf3dd6f8a04acfd4dd92c8d250835855a2;hb=0a5854b381b30670ba749b8575bc85548a10578d;hp=9a6e201d75e24d366903ff4e937f80d71e45303c;hpb=9360df156b23158232dca10ffdb8a8ffdcaf0930;p=samtools.git

diff --git a/sam.c b/sam.c
index 9a6e201..45cb05c 100644
--- a/sam.c
+++ b/sam.c
@@ -19,8 +19,21 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
 		h->target_len[i] = h0->target_len[i];
 		h->target_name[i] = strdup(h0->target_name[i]);
 	}
+	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)
 {
@@ -39,18 +52,23 @@ 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");
 			} else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
 		}
+		sam_header_parse_rg(fp->header);
 	} else if (mode[0] == 'w') { // write
 		fp->header = bam_header_dup((const bam_header_t*)aux);
 		if (mode[1] == 'b') { // binary
+			char bmode[3];
+			bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
 			fp->type |= TYPE_BAM;
-			fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w");
+			fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
 			if (fp->x.bam == 0) goto open_err_ret;
 			bam_header_write(fp->x.bam, fp->header);
 		} else { // text
@@ -116,7 +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;
@@ -125,8 +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);