+++ /dev/null
-#include <string.h>
-#include <stdlib.h>
-#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 <in.glf>\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
projects / samtools.git / blobdiff