X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.c;h=07524c0213b30bcae3870f8424da38daef43ac49;hb=d0e30eec1158752010659982342a611fc91ae8e3;hp=d53aa0eacd47b24ebf74629e7d15c5d88a6cfcc6;hpb=21cb882e9cbf5a43f1de4143e0661a038ab83748;p=samtools.git

diff --git a/sam.c b/sam.c
index d53aa0e..07524c0 100644
--- a/sam.c
+++ b/sam.c
@@ -1,4 +1,6 @@
 #include <string.h>
+#include <unistd.h>
+#include "faidx.h"
 #include "sam.h"
 
 #define TYPE_BAM  1
@@ -19,13 +21,13 @@ 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);
@@ -74,6 +76,9 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 			// open file
 			fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
 			if (fp->x.tamr == 0) goto open_err_ret;
+			if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
+			else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
+			else fp->type |= BAM_OFDEC<<2;
 			// write header
 			if (strstr(mode, "h")) {
 				int i;
@@ -125,7 +130,7 @@ int samwrite(samfile_t *fp, const bam1_t *b)
 	if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
 	if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
 	else {
-		char *s = bam_format1(fp->header, b);
+		char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
 		int l = strlen(s);
 		fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
 		free(s);
@@ -148,3 +153,23 @@ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
 	bam_destroy1(b);
 	return 0;
 }
+
+char *samfaipath(const char *fn_ref)
+{
+	char *fn_list = 0;
+	if (fn_ref == 0) return 0;
+	fn_list = calloc(strlen(fn_ref) + 5, 1);
+	strcat(strcpy(fn_list, fn_ref), ".fai");
+	if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
+		if (access(fn_ref, R_OK) == -1) {
+			fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
+		} else {
+			fprintf(stderr, "[samfaipath] build FASTA index...\n");
+			if (fai_build(fn_ref) == -1) {
+				fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
+				free(fn_list); fn_list = 0;
+			}
+		}
+	}
+	return fn_list;
+}