X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_import.c;fp=samtools%2Fbam_import.c;h=0000000000000000000000000000000000000000;hp=9d84328bdbdafb5f4e76a19e7edf176121aca5b4;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a

diff --git a/samtools/bam_import.c b/samtools/bam_import.c
deleted file mode 100644
index 9d84328..0000000
--- a/samtools/bam_import.c
+++ /dev/null
@@ -1,459 +0,0 @@
-#include <zlib.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <string.h>
-#include <stdlib.h>
-#include <unistd.h>
-#include <assert.h>
-#ifdef _WIN32
-#include <fcntl.h>
-#endif
-#include "kstring.h"
-#include "bam.h"
-#include "sam_header.h"
-#include "kseq.h"
-#include "khash.h"
-
-KSTREAM_INIT(gzFile, gzread, 8192)
-KHASH_MAP_INIT_STR(ref, uint64_t)
-
-void bam_init_header_hash(bam_header_t *header);
-void bam_destroy_header_hash(bam_header_t *header);
-int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);
-
-unsigned char bam_nt16_table[256] = {
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-	 1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
-	15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
-	15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
-	15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
-	15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
-	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
-};
-
-unsigned short bam_char2flag_table[256] = {
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
-	BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
-	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
-};
-
-char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
-
-struct __tamFile_t {
-	gzFile fp;
-	kstream_t *ks;
-	kstring_t *str;
-	uint64_t n_lines;
-	int is_first;
-};
-
-char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
-{
-	char **list = 0, *s;
-	int n = 0, dret, m = 0;
-	gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
-	kstream_t *ks;
-	kstring_t *str;
-	str = (kstring_t*)calloc(1, sizeof(kstring_t));
-	ks = ks_init(fp);
-	while (ks_getuntil(ks, '\n', str, &dret) > 0) {
-		if (n == m) {
-			m = m? m << 1 : 16;
-			list = (char**)realloc(list, m * sizeof(char*));
-		}
-		if (str->s[str->l-1] == '\r')
-			str->s[--str->l] = '\0';
-		s = list[n++] = (char*)calloc(str->l + 1, 1);
-		strcpy(s, str->s);
-	}
-	ks_destroy(ks);
-	gzclose(fp);
-	free(str->s); free(str);
-	*_n = n;
-	return list;
-}
-
-static bam_header_t *hash2header(const kh_ref_t *hash)
-{
-	bam_header_t *header;
-	khiter_t k;
-	header = bam_header_init();
-	header->n_targets = kh_size(hash);
-	header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
-	header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
-	for (k = kh_begin(hash); k != kh_end(hash); ++k) {
-		if (kh_exist(hash, k)) {
-			int i = (int)kh_value(hash, k);
-			header->target_name[i] = (char*)kh_key(hash, k);
-			header->target_len[i] = kh_value(hash, k)>>32;
-		}
-	}
-	bam_init_header_hash(header);
-	return header;
-}
-bam_header_t *sam_header_read2(const char *fn)
-{
-	bam_header_t *header;
-	int c, dret, ret, error = 0;
-	gzFile fp;
-	kstream_t *ks;
-	kstring_t *str;
-	kh_ref_t *hash;
-	khiter_t k;
-	if (fn == 0) return 0;
-	fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
-	if (fp == 0) return 0;
-	hash = kh_init(ref);
-	ks = ks_init(fp);
-	str = (kstring_t*)calloc(1, sizeof(kstring_t));
-	while (ks_getuntil(ks, 0, str, &dret) > 0) {
-		char *s = strdup(str->s);
-		int len, i;
-		i = kh_size(hash);
-		ks_getuntil(ks, 0, str, &dret);
-		len = atoi(str->s);
-		k = kh_put(ref, hash, s, &ret);
-		if (ret == 0) {
-			fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
-			error = 1;
-		}
-		kh_value(hash, k) = (uint64_t)len<<32 | i;
-		if (dret != '\n')
-			while ((c = ks_getc(ks)) != '\n' && c != -1);
-	}
-	ks_destroy(ks);
-	gzclose(fp);
-	free(str->s); free(str);
-	fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
-	if (error) return 0;
-	header = hash2header(hash);
-	kh_destroy(ref, hash);
-	return header;
-}
-static inline uint8_t *alloc_data(bam1_t *b, int size)
-{
-	if (b->m_data < size) {
-		b->m_data = size;
-		kroundup32(b->m_data);
-		b->data = (uint8_t*)realloc(b->data, b->m_data);
-	}
-	return b->data;
-}
-static inline void parse_error(int64_t n_lines, const char * __restrict msg)
-{
-	fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
-	abort();
-}
-static inline void append_text(bam_header_t *header, kstring_t *str)
-{
-	size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
-	kroundup32(x); kroundup32(y);
-	if (x < y) 
-    {
-        header->n_text = y;
-        header->text = (char*)realloc(header->text, y);
-        if ( !header->text ) 
-        {
-            fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
-            abort();
-        }
-    }
-    // Sanity check
-    if ( header->l_text+str->l+1 >= header->n_text )
-    {
-        fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,header->n_text,x,y);
-        abort();
-    }
-	strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
-	header->l_text += str->l + 1;
-	header->text[header->l_text] = 0;
-}
-
-int sam_header_parse(bam_header_t *h)
-{
-	char **tmp;
-	int i;
-	free(h->target_len); free(h->target_name);
-	h->n_targets = 0; h->target_len = 0; h->target_name = 0;
-	if (h->l_text < 3) return 0;
-	if (h->dict == 0) h->dict = sam_header_parse2(h->text);
-	tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
-	if (h->n_targets == 0) return 0;
-	h->target_name = calloc(h->n_targets, sizeof(void*));
-	for (i = 0; i < h->n_targets; ++i)
-		h->target_name[i] = strdup(tmp[i]);
-	free(tmp);
-	tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
-	h->target_len = calloc(h->n_targets, 4);
-	for (i = 0; i < h->n_targets; ++i)
-		h->target_len[i] = atoi(tmp[i]);
-	free(tmp);
-	return h->n_targets;
-}
-
-bam_header_t *sam_header_read(tamFile fp)
-{
-	int ret, dret;
-	bam_header_t *header = bam_header_init();
-	kstring_t *str = fp->str;
-	while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
-		str->s[str->l] = dret; // note that str->s is NOT null terminated!!
-		append_text(header, str);
-		if (dret != '\n') {
-			ret = ks_getuntil(fp->ks, '\n', str, &dret);
-			str->s[str->l] = '\n'; // NOT null terminated!!
-			append_text(header, str);
-		}
-		++fp->n_lines;
-	}
-	sam_header_parse(header);
-	bam_init_header_hash(header);
-	fp->is_first = 1;
-	return header;
-}
-
-int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
-{
-	int ret, doff, doff0, dret, z = 0;
-	bam1_core_t *c = &b->core;
-	kstring_t *str = fp->str;
-	kstream_t *ks = fp->ks;
-
-	if (fp->is_first) {
-		fp->is_first = 0;
-		ret = str->l;
-	} else {
-		do { // special consideration for empty lines
-			ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
-			if (ret >= 0) z += str->l + 1;
-		} while (ret == 0);
-	}
-	if (ret < 0) return -1;
-	++fp->n_lines;
-	doff = 0;
-
-	{ // name
-		c->l_qname = strlen(str->s) + 1;
-		memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
-		doff += c->l_qname;
-	}
-	{ // flag
-		long flag;
-		char *s;
-		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
-		flag = strtol((char*)str->s, &s, 0);
-		if (*s) { // not the end of the string
-			flag = 0;
-			for (s = str->s; *s; ++s)
-				flag |= bam_char2flag_table[(int)*s];
-		}
-		c->flag = flag;
-	}
-	{ // tid, pos, qual
-		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
-		if (c->tid < 0 && strcmp(str->s, "*")) {
-			if (header->n_targets == 0) {
-				fprintf(stderr, "[sam_read1] missing header? Abort!\n");
-				exit(1);
-			} else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
-		}
-		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
-		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
-		if (ret < 0) return -2;
-	}
-	{ // cigar
-		char *s, *t;
-		int i, op;
-		long x;
-		c->n_cigar = 0;
-		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
-		z += str->l + 1;
-		if (str->s[0] != '*') {
-			for (s = str->s; *s; ++s) {
-				if (isalpha(*s)) ++c->n_cigar;
-				else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
-			}
-			b->data = alloc_data(b, doff + c->n_cigar * 4);
-			for (i = 0, s = str->s; i != c->n_cigar; ++i) {
-				x = strtol(s, &t, 10);
-				op = toupper(*t);
-				if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
-				else if (op == 'I') op = BAM_CINS;
-				else if (op == 'D') op = BAM_CDEL;
-				else if (op == 'N') op = BAM_CREF_SKIP;
-				else if (op == 'S') op = BAM_CSOFT_CLIP;
-				else if (op == 'H') op = BAM_CHARD_CLIP;
-				else if (op == 'P') op = BAM_CPAD;
-				else parse_error(fp->n_lines, "invalid CIGAR operation");
-				s = t + 1;
-				bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
-			}
-			if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
-			c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
-			doff += c->n_cigar * 4;
-		} else {
-			if (!(c->flag&BAM_FUNMAP)) {
-				fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
-				c->flag |= BAM_FUNMAP;
-			}
-			c->bin = bam_reg2bin(c->pos, c->pos + 1);
-		}
-	}
-	{ // mtid, mpos, isize
-		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
-		c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
-		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
-		c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
-		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
-		c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
-		if (ret < 0) return -4;
-	}
-	{ // seq and qual
-		int i;
-		uint8_t *p = 0;
-		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
-		z += str->l + 1;
-		if (strcmp(str->s, "*")) {
-			c->l_qseq = strlen(str->s);
-			if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
-				parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
-			p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
-			memset(p, 0, (c->l_qseq+1)/2);
-			for (i = 0; i < c->l_qseq; ++i)
-				p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
-		} else c->l_qseq = 0;
-		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
-		z += str->l + 1;
-		if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
-			parse_error(fp->n_lines, "sequence and quality are inconsistent");
-		p += (c->l_qseq+1)/2;
-		if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
-		else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
-		doff += c->l_qseq + (c->l_qseq+1)/2;
-	}
-	doff0 = doff;
-	if (dret != '\n' && dret != '\r') { // aux
-		while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
-			uint8_t *s, type, key[2];
-			z += str->l + 1;
-			if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
-				parse_error(fp->n_lines, "missing colon in auxiliary data");
-			key[0] = str->s[0]; key[1] = str->s[1];
-			type = str->s[3];
-			s = alloc_data(b, doff + 3) + doff;
-			s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
-			if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
-				s = alloc_data(b, doff + 2) + doff;
-				*s++ = 'A'; *s = str->s[5];
-				doff += 2;
-			} else if (type == 'I' || type == 'i') {
-				long long x;
-				s = alloc_data(b, doff + 5) + doff;
-				x = (long long)atoll(str->s + 5);
-				if (x < 0) {
-					if (x >= -127) {
-						*s++ = 'c'; *(int8_t*)s = (int8_t)x;
-						s += 1; doff += 2;
-					} else if (x >= -32767) {
-						*s++ = 's'; *(int16_t*)s = (int16_t)x;
-						s += 2; doff += 3;
-					} else {
-						*s++ = 'i'; *(int32_t*)s = (int32_t)x;
-						s += 4; doff += 5;
-						if (x < -2147483648ll)
-							fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
-									(long long)fp->n_lines, x);
-					}
-				} else {
-					if (x <= 255) {
-						*s++ = 'C'; *s++ = (uint8_t)x;
-						doff += 2;
-					} else if (x <= 65535) {
-						*s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
-						s += 2; doff += 3;
-					} else {
-						*s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
-						s += 4; doff += 5;
-						if (x > 4294967295ll)
-							fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
-									(long long)fp->n_lines, x);
-					}
-				}
-			} else if (type == 'f') {
-				s = alloc_data(b, doff + 5) + doff;
-				*s++ = 'f';
-				*(float*)s = (float)atof(str->s + 5);
-				s += 4; doff += 5;
-			} else if (type == 'd') {
-				s = alloc_data(b, doff + 9) + doff;
-				*s++ = 'd';
-				*(float*)s = (float)atof(str->s + 9);
-				s += 8; doff += 9;
-			} else if (type == 'Z' || type == 'H') {
-				int size = 1 + (str->l - 5) + 1;
-				if (type == 'H') { // check whether the hex string is valid
-					int i;
-					if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
-					for (i = 0; i < str->l - 5; ++i) {
-						int c = toupper(str->s[5 + i]);
-						if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
-							parse_error(fp->n_lines, "invalid hex character");
-					}
-				}
-				s = alloc_data(b, doff + size) + doff;
-				*s++ = type;
-				memcpy(s, str->s + 5, str->l - 5);
-				s[str->l - 5] = 0;
-				doff += size;
-			} else parse_error(fp->n_lines, "unrecognized type");
-			if (dret == '\n' || dret == '\r') break;
-		}
-	}
-	b->l_aux = doff - doff0;
-	b->data_len = doff;
-	return z;
-}
-
-tamFile sam_open(const char *fn)
-{
-	tamFile fp;
-	gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
-	if (gzfp == 0) return 0;
-	fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
-	fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
-	fp->fp = gzfp;
-	fp->ks = ks_init(fp->fp);
-	return fp;
-}
-
-void sam_close(tamFile fp)
-{
-	if (fp) {
-		ks_destroy(fp->ks);
-		gzclose(fp->fp);
-		free(fp->str->s); free(fp->str);
-		free(fp);
-	}
-}