Mercurial > repos > xilinxu > xilinxu
diff bwa-0.7.9a/bamlite.c @ 0:ce5a8082bbb8 draft
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author | xilinxu |
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date | Thu, 14 Aug 2014 02:16:48 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa-0.7.9a/bamlite.c Thu Aug 14 02:16:48 2014 -0400 @@ -0,0 +1,210 @@ +#include <stdlib.h> +#include <ctype.h> +#include <string.h> +#include <stdio.h> +#include <errno.h> +#include "bamlite.h" + +#ifdef USE_MALLOC_WRAPPERS +# include "malloc_wrap.h" +#endif + +/********************* + * from bam_endian.c * + *********************/ + +static inline int bam_is_big_endian() +{ + long one= 1; + return !(*((char *)(&one))); +} +static inline uint16_t bam_swap_endian_2(uint16_t v) +{ + return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8)); +} +static inline void *bam_swap_endian_2p(void *x) +{ + *(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x); + return x; +} +static inline uint32_t bam_swap_endian_4(uint32_t v) +{ + v = ((v & 0x0000FFFFU) << 16) | (v >> 16); + return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8); +} +static inline void *bam_swap_endian_4p(void *x) +{ + *(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x); + return x; +} +static inline uint64_t bam_swap_endian_8(uint64_t v) +{ + v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32); + v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16); + return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8); +} +static inline void *bam_swap_endian_8p(void *x) +{ + *(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x); + return x; +} + +/************** + * from bam.c * + **************/ + +int bam_is_be; + +bam_header_t *bam_header_init() +{ + bam_is_be = bam_is_big_endian(); + return (bam_header_t*)calloc(1, sizeof(bam_header_t)); +} + +void bam_header_destroy(bam_header_t *header) +{ + int32_t i; + if (header == 0) return; + if (header->target_name) { + for (i = 0; i < header->n_targets; ++i) + if (header->target_name[i]) free(header->target_name[i]); + if (header->target_len) free(header->target_len); + free(header->target_name); + } + if (header->text) free(header->text); + free(header); +} + +bam_header_t *bam_header_read(bamFile fp) +{ + bam_header_t *header; + char buf[4]; + int magic_len; + int32_t i = 1, name_len; + // read "BAM1" + magic_len = bam_read(fp, buf, 4); + if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) { + fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n"); + return NULL; + } + header = bam_header_init(); + // read plain text and the number of reference sequences + if (bam_read(fp, &header->l_text, 4) != 4) goto fail; + if (bam_is_be) bam_swap_endian_4p(&header->l_text); + header->text = (char*)calloc(header->l_text + 1, 1); + if (bam_read(fp, header->text, header->l_text) != header->l_text) goto fail; + if (bam_read(fp, &header->n_targets, 4) != 4) goto fail; + if (bam_is_be) bam_swap_endian_4p(&header->n_targets); + // read reference sequence names and lengths + header->target_name = (char**)calloc(header->n_targets, sizeof(char*)); + header->target_len = (uint32_t*)calloc(header->n_targets, 4); + for (i = 0; i != header->n_targets; ++i) { + if (bam_read(fp, &name_len, 4) != 4) goto fail; + if (bam_is_be) bam_swap_endian_4p(&name_len); + header->target_name[i] = (char*)calloc(name_len, 1); + if (bam_read(fp, header->target_name[i], name_len) != name_len) { + goto fail; + } + if (bam_read(fp, &header->target_len[i], 4) != 4) goto fail; + if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]); + } + return header; + fail: + bam_header_destroy(header); + return NULL; +} + +static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data) +{ + uint8_t *s; + uint32_t i, *cigar = (uint32_t*)(data + c->l_qname); + s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2; + for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]); + while (s < data + data_len) { + uint8_t type; + s += 2; // skip key + type = toupper(*s); ++s; // skip type + if (type == 'C' || type == 'A') ++s; + else if (type == 'S') { bam_swap_endian_2p(s); s += 2; } + else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; } + else if (type == 'D') { bam_swap_endian_8p(s); s += 8; } + else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; } + } +} + +int bam_read1(bamFile fp, bam1_t *b) +{ + bam1_core_t *c = &b->core; + int32_t block_len, ret, i; + uint32_t x[8]; + + if ((ret = bam_read(fp, &block_len, 4)) != 4) { + if (ret == 0) return -1; // normal end-of-file + else return -2; // truncated + } + if (bam_read(fp, x, sizeof(bam1_core_t)) != sizeof(bam1_core_t)) return -3; + if (bam_is_be) { + bam_swap_endian_4p(&block_len); + for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i); + } + c->tid = x[0]; c->pos = x[1]; + c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff; + c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff; + c->l_qseq = x[4]; + c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7]; + b->data_len = block_len - sizeof(bam1_core_t); + if (b->m_data < b->data_len) { + b->m_data = b->data_len; + kroundup32(b->m_data); + b->data = (uint8_t*)realloc(b->data, b->m_data); + } + if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4; + b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2; + if (bam_is_be) swap_endian_data(c, b->data_len, b->data); + return 4 + block_len; +} + + +#ifdef USE_VERBOSE_ZLIB_WRAPPERS +// Versions of gzopen, gzread and gzclose that print up error messages + +gzFile bamlite_gzopen(const char *fn, const char *mode) { + gzFile fp; + if (strcmp(fn, "-") == 0) { + fp = gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode); + if (!fp) { + fprintf(stderr, "Couldn't open %s : %s", + (strstr(mode, "r"))? "stdin" : "stdout", + strerror(errno)); + } + return fp; + } + if ((fp = gzopen(fn, mode)) == 0) { + fprintf(stderr, "Couldn't open %s : %s\n", fn, + errno ? strerror(errno) : "Out of memory"); + } + return fp; +} + +int bamlite_gzread(gzFile file, void *ptr, unsigned int len) { + int ret = gzread(file, ptr, len); + + if (ret < 0) { + int errnum = 0; + const char *msg = gzerror(file, &errnum); + fprintf(stderr, "gzread error: %s\n", + Z_ERRNO == errnum ? strerror(errno) : msg); + } + return ret; +} + +int bamlite_gzclose(gzFile file) { + int ret = gzclose(file); + if (Z_OK != ret) { + fprintf(stderr, "gzclose error: %s\n", + Z_ERRNO == ret ? strerror(errno) : zError(ret)); + } + + return ret; +} +#endif /* USE_VERBOSE_ZLIB_WRAPPERS */