X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=glf.c;fp=glf.c;h=0000000000000000000000000000000000000000;hp=8d5346ae70af825afeeefaa2d50f276749d5301f;hb=e2bd290b8643f0a728c282a8b825392307750210;hpb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5 diff --git a/glf.c b/glf.c deleted file mode 100644 index 8d5346a..0000000 --- a/glf.c +++ /dev/null @@ -1,236 +0,0 @@ -#include -#include -#include "glf.h" - -#ifdef _NO_BGZF -// then alias bgzf_*() functions -#endif - -static int glf3_is_BE = 0; - -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 uint16_t bam_swap_endian_2(uint16_t v) -{ - return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8)); -} - -static inline int bam_is_big_endian() -{ - long one= 1; - return !(*((char *)(&one))); -} - -glf3_header_t *glf3_header_init() -{ - glf3_is_BE = bam_is_big_endian(); - return (glf3_header_t*)calloc(1, sizeof(glf3_header_t)); -} - -glf3_header_t *glf3_header_read(glfFile fp) -{ - glf3_header_t *h; - char magic[4]; - h = glf3_header_init(); - bgzf_read(fp, magic, 4); - if (strncmp(magic, "GLF\3", 4)) { - fprintf(stderr, "[glf3_header_read] invalid magic.\n"); - glf3_header_destroy(h); - return 0; - } - bgzf_read(fp, &h->l_text, 4); - if (glf3_is_BE) h->l_text = bam_swap_endian_4(h->l_text); - if (h->l_text) { - h->text = (uint8_t*)calloc(h->l_text + 1, 1); - bgzf_read(fp, h->text, h->l_text); - } - return h; -} - -void glf3_header_write(glfFile fp, const glf3_header_t *h) -{ - int32_t x; - bgzf_write(fp, "GLF\3", 4); - x = glf3_is_BE? bam_swap_endian_4(h->l_text) : h->l_text; - bgzf_write(fp, &x, 4); - if (h->l_text) bgzf_write(fp, h->text, h->l_text); -} - -void glf3_header_destroy(glf3_header_t *h) -{ - free(h->text); - free(h); -} - -char *glf3_ref_read(glfFile fp, int *len) -{ - int32_t n, x; - char *str; - *len = 0; - if (bgzf_read(fp, &n, 4) != 4) return 0; - if (glf3_is_BE) n = bam_swap_endian_4(n); - if (n < 0) { - fprintf(stderr, "[glf3_ref_read] invalid reference name length: %d.\n", n); - return 0; - } - str = (char*)calloc(n + 1, 1); // not necesarily n+1 in fact - x = bgzf_read(fp, str, n); - x += bgzf_read(fp, len, 4); - if (x != n + 4) { - free(str); *len = -1; return 0; // truncated - } - if (glf3_is_BE) *len = bam_swap_endian_4(*len); - return str; -} - -void glf3_ref_write(glfFile fp, const char *str, int len) -{ - int32_t m, n = strlen(str) + 1; - m = glf3_is_BE? bam_swap_endian_4(n) : n; - bgzf_write(fp, &m, 4); - bgzf_write(fp, str, n); - if (glf3_is_BE) len = bam_swap_endian_4(len); - bgzf_write(fp, &len, 4); -} - -void glf3_view1(const char *ref_name, const glf3_t *g3, int pos) -{ - int j; - if (g3->rtype == GLF3_RTYPE_END) return; - printf("%s\t%d\t%c\t%d\t%d\t%d", ref_name, pos + 1, - g3->rtype == GLF3_RTYPE_INDEL? '*' : "XACMGRSVTWYHKDBN"[g3->ref_base], - g3->depth, g3->rms_mapQ, g3->min_lk); - if (g3->rtype == GLF3_RTYPE_SUB) - for (j = 0; j != 10; ++j) printf("\t%d", g3->lk[j]); - else { - printf("\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t", g3->lk[0], g3->lk[1], g3->lk[2], g3->indel_len[0], g3->indel_len[1], - g3->indel_len[0]? g3->indel_seq[0] : "*", g3->indel_len[1]? g3->indel_seq[1] : "*"); - } - printf("\n"); -} - -int glf3_write1(glfFile fp, const glf3_t *g3) -{ - int r; - uint8_t c; - uint32_t y[2]; - c = g3->rtype<<4 | g3->ref_base; - r = bgzf_write(fp, &c, 1); - if (g3->rtype == GLF3_RTYPE_END) return r; - y[0] = g3->offset; - y[1] = g3->min_lk<<24 | g3->depth; - if (glf3_is_BE) { - y[0] = bam_swap_endian_4(y[0]); - y[1] = bam_swap_endian_4(y[1]); - } - r += bgzf_write(fp, y, 8); - r += bgzf_write(fp, &g3->rms_mapQ, 1); - if (g3->rtype == GLF3_RTYPE_SUB) r += bgzf_write(fp, g3->lk, 10); - else { - int16_t x[2]; - r += bgzf_write(fp, g3->lk, 3); - x[0] = glf3_is_BE? bam_swap_endian_2(g3->indel_len[0]) : g3->indel_len[0]; - x[1] = glf3_is_BE? bam_swap_endian_2(g3->indel_len[1]) : g3->indel_len[1]; - r += bgzf_write(fp, x, 4); - if (g3->indel_len[0]) r += bgzf_write(fp, g3->indel_seq[0], abs(g3->indel_len[0])); - if (g3->indel_len[1]) r += bgzf_write(fp, g3->indel_seq[1], abs(g3->indel_len[1])); - } - return r; -} - -#ifndef kv_roundup32 -#define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) -#endif - -int glf3_read1(glfFile fp, glf3_t *g3) -{ - int r; - uint8_t c; - uint32_t y[2]; - r = bgzf_read(fp, &c, 1); - if (r == 0) return 0; - g3->ref_base = c & 0xf; - g3->rtype = c>>4; - if (g3->rtype == GLF3_RTYPE_END) return r; - r += bgzf_read(fp, y, 8); - if (glf3_is_BE) { - y[0] = bam_swap_endian_4(y[0]); - y[1] = bam_swap_endian_4(y[1]); - } - g3->offset = y[0]; - g3->min_lk = y[1]>>24; - g3->depth = y[1]<<8>>8; - r += bgzf_read(fp, &g3->rms_mapQ, 1); - if (g3->rtype == GLF3_RTYPE_SUB) r += bgzf_read(fp, g3->lk, 10); - else { - int16_t x[2], max; - r += bgzf_read(fp, g3->lk, 3); - r += bgzf_read(fp, x, 4); - if (glf3_is_BE) { - x[0] = bam_swap_endian_2(x[0]); - x[1] = bam_swap_endian_2(x[1]); - } - g3->indel_len[0] = x[0]; - g3->indel_len[1] = x[1]; - x[0] = abs(x[0]); x[1] = abs(x[1]); - max = (x[0] > x[1]? x[0] : x[1]) + 1; - if (g3->max_len < max) { - g3->max_len = max; - kv_roundup32(g3->max_len); - g3->indel_seq[0] = (char*)realloc(g3->indel_seq[0], g3->max_len); - g3->indel_seq[1] = (char*)realloc(g3->indel_seq[1], g3->max_len); - } - r += bgzf_read(fp, g3->indel_seq[0], x[0]); - r += bgzf_read(fp, g3->indel_seq[1], x[1]); - g3->indel_seq[0][x[0]] = g3->indel_seq[1][x[1]] = 0; - } - return r; -} - -void glf3_view(glfFile fp) -{ - glf3_header_t *h; - char *name; - glf3_t *g3; - int len; - h = glf3_header_read(fp); - g3 = glf3_init1(); - while ((name = glf3_ref_read(fp, &len)) != 0) { - int pos = 0; - while (glf3_read1(fp, g3) && g3->rtype != GLF3_RTYPE_END) { - pos += g3->offset; - glf3_view1(name, g3, pos); - } - free(name); - } - glf3_header_destroy(h); - glf3_destroy1(g3); -} - -int glf3_view_main(int argc, char *argv[]) -{ - glfFile fp; - if (argc == 1) { - fprintf(stderr, "Usage: glfview \n"); - return 1; - } - fp = (strcmp(argv[1], "-") == 0)? bgzf_fdopen(fileno(stdin), "r") : bgzf_open(argv[1], "r"); - if (fp == 0) { - fprintf(stderr, "Fail to open file '%s'\n", argv[1]); - return 1; - } - glf3_view(fp); - bgzf_close(fp); - return 0; -} - -#ifdef GLFVIEW_MAIN -int main(int argc, char *argv[]) -{ - return glf3_view_main(argc, argv); -} -#endif