--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/sam.c	Wed Oct 12 19:50:38 2011 -0400
@@ -0,0 +1,176 @@
+#include <string.h>
+#include <unistd.h>
+#include "faidx.h"
+#include "sam.h"
+
+#define TYPE_BAM  1
+#define TYPE_READ 2
+
+bam_header_t *bam_header_dup(const bam_header_t *h0)
+{
+	bam_header_t *h;
+	int i;
+	h = bam_header_init();
+	*h = *h0;
+	h->hash = 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);
+	h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
+	for (i = 0; i < h->n_targets; ++i) {
+		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)
+{
+	samfile_t *fp;
+	fp = (samfile_t*)calloc(1, sizeof(samfile_t));
+	if (mode[0] == 'r') { // read
+		fp->type |= TYPE_READ;
+		if (mode[1] == 'b') { // binary
+			fp->type |= TYPE_BAM;
+			fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
+			if (fp->x.bam == 0) goto open_err_ret;
+			fp->header = bam_header_read(fp->x.bam);
+		} else { // text
+			fp->x.tamr = sam_open(fn);
+			if (fp->x.tamr == 0) goto open_err_ret;
+			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_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, 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;
+				bam_header_t *alt;
+				// parse the header text 
+				alt = bam_header_init();
+				alt->l_text = fp->header->l_text; alt->text = fp->header->text;
+				sam_header_parse(alt);
+				alt->l_text = 0; alt->text = 0;
+				// check if there are @SQ lines in the header
+				fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
+				if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
+					if (alt->n_targets != fp->header->n_targets)
+						fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
+				} else { // then dump ->target_{name,len}
+					for (i = 0; i < fp->header->n_targets; ++i)
+						fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
+				}
+				bam_header_destroy(alt);
+			}
+		}
+	}
+	return fp;
+
+open_err_ret:
+	free(fp);
+	return 0;
+}
+
+void samclose(samfile_t *fp)
+{
+	if (fp == 0) return;
+	if (fp->header) bam_header_destroy(fp->header);
+	if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
+	else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
+	else fclose(fp->x.tamw);
+	free(fp);
+}
+
+int samread(samfile_t *fp, bam1_t *b)
+{
+	if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
+	if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
+	else return sam_read1(fp->x.tamr, fp->header, b);
+}
+
+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_core(fp->header, b, fp->type>>2&3);
+		int l = strlen(s);
+		fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
+		free(s);
+		return l + 1;
+	}
+}
+
+int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
+{
+	bam_plbuf_t *buf;
+	int ret;
+	bam1_t *b;
+	b = bam_init1();
+	buf = bam_plbuf_init(func, func_data);
+	bam_plbuf_set_mask(buf, mask);
+	while ((ret = samread(fp, b)) >= 0)
+		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;
+}