X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.c;h=ecdee02dddb98a32d47a59e3154179356acecadf;hb=205b696ea778f5b7cfe70e5531bfe6583b5af333;hp=9a6e201d75e24d366903ff4e937f80d71e45303c;hpb=9360df156b23158232dca10ffdb8a8ffdcaf0930;p=samtools.git

diff --git a/sam.c b/sam.c
index 9a6e201..ecdee02 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
@@ -10,7 +12,7 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
 	int i;
 	h = bam_header_init();
 	*h = *h0;
-	h->hash = 0;
+	h->hash = h->dict = h->rg2lib = 0;
 	h->text = (char*)calloc(h->l_text + 1, 1);
 	memcpy(h->text, h0->text, h->l_text);
 	h->target_len = (uint32_t*)calloc(h->n_targets, 4);
@@ -21,6 +23,18 @@ bam_header_t *bam_header_dup(const bam_header_t *h0)
 	}
 	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)
 {
@@ -39,8 +53,11 @@ 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);
+					if (fp->header == 0) goto open_err_ret;
+					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");
@@ -49,14 +66,19 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 	} 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
 			// 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;
@@ -108,7 +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);
@@ -116,7 +138,7 @@ 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;
@@ -125,10 +147,29 @@ 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);
 	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;
+}