File: sam.c

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#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 = 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);
	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]);
	}
	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;
}

int samthreads(samfile_t *fp, int n_threads, int n_sub_blks)
{
	if (!(fp->type&1) || (fp->type&2)) return -1;
	bgzf_mt(fp->x.bam, n_threads, n_sub_blks);
	return 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 (strchr(mode, 'r')) { // read
		fp->type |= TYPE_READ;
		if (strchr(mode, '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);
					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 && bam_verbose >= 1)
					fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
			} else if (bam_verbose >= 2) fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
		}
	} else if (strchr(mode, 'w')) { // write
		fp->header = bam_header_dup((const bam_header_t*)aux);
		if (strchr(mode, 'b')) { // binary
			char bmode[3];
			int i, compress_level = -1;
			for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break;
			if (mode[i]) compress_level = mode[i] - '0';
			if (strchr(mode, 'u')) compress_level = 0;
			bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '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.tamw == 0) goto open_err_ret;
			if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2;
			else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2;
			else fp->type |= BAM_OFDEC<<2;
			// write header
			if (strchr(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); // FIXME: better to skip the trailing NULL
				if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
					if (alt->n_targets != fp->header->n_targets && bam_verbose >= 1)
						fprintf(stderr, "[samopen] inconsistent number of target sequences. Output the text header.\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 {
			if (bam_verbose >= 3) 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;
}