#include <string.h>

//#include <unistd.h>

#include <stdlib.h>

#include <stdio.h>

#include <sys/stat.h>

#include <errno.h>

#include "bgzf.h"

#include "tabix.h"

#include "knetfile.h"

#include "glibc_win64_flat/getopt.h"

#include <Windows.h>

#define strcasecmp _stricmp

#define PACKAGE_VERSION "0.2.5 (r1005)"

#define error(...) { fprintf(stderr,__VA_ARGS__); return -1; }

int reheader_file(const char *header, const char *file, int meta)

{

char *buffer;

int skip_until = 0;

FILE *fh;

int page_size;

char *buf;

BGZF *bgzf_out;

ssize_t nread;

BGZF *fp = bgzf_open(file,"r");

if (bgzf_read_block(fp) != 0 || !fp->block_length)

return -1;

buffer = fp->uncompressed_block;

if ( buffer[0]==meta )

{

skip_until = 1;

// Skip the header

while (1)

{

if ( buffer[skip_until]=='\n' )

{

skip_until++;

if ( skip_until>=fp->block_length )

{

if (bgzf_read_block(fp) != 0 || !fp->block_length)

error("no body?\n");

skip_until = 0;

}

// The header has finished

if ( buffer[skip_until]!=meta ) break;

}

skip_until++;

if ( skip_until>=fp->block_length )

{

if (bgzf_read_block(fp) != 0 || !fp->block_length)

error("no body?\n");

skip_until = 0;

}

}

}

fh = fopen(header,"r");

if ( !fh )

error("%s: %s", header,strerror(errno));

page_size = getpagesize();

buf = malloc(page_size); //Dong Code

bgzf_out = bgzf_dopen(fileno(stdout), "w");

while ( (nread=fread(buf,1,page_size-1,fh))>0 )

{

if ( nread<page_size-1 && buf[nread-1]!='\n' )

buf[nread++] = '\n';

if (bgzf_write(bgzf_out, buf, nread) < 0) error("Error: %d\n",bgzf_out->errcode);

}

fclose(fh);

if ( fp->block_length - skip_until > 0 )

{

if (bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until) < 0)

error("Error: %d\n",fp->errcode);

}

if (bgzf_flush(bgzf_out) < 0)

error("Error: %d\n",bgzf_out->errcode);

while (1)

{

int count;

#ifdef _USE_KNETFILE

nread = knet_read(fp->fp, buf, page_size);

#else

nread = fread(buf, 1, page_size, fp->fp);

#endif

if ( nread<=0 )

break;

count = fwrite(buf, 1, nread, bgzf_out->fp);

if (count != nread)

error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread);

}

if (bgzf_close(bgzf_out) < 0)

error("Error: %d\n",bgzf_out->errcode);

return 0;

}

int main(int argc, char *argv[])

{

int c, skip = -1, meta = -1, list_chrms = 0, force = 0, print_header = 0, print_only_header = 0, bed_reg = 0;

ti_conf_t conf = ti_conf_gff, *conf_ptr = NULL;

const char *reheader = NULL;

struct __stat64 stat_tbi,stat_vcf;

char *fnidx;

while ((c = getopt(argc, argv, "p:s:b:e:0S:c:lhHfBr:")) >= 0) {

switch (c) {

case 'B': bed_reg = 1; break;

case '0': conf.preset |= TI_FLAG_UCSC; break;

case 'S': skip = atoi(optarg); break;

case 'c': meta = optarg[0]; break;

case 'p':

if (strcmp(optarg, "gff") == 0) conf_ptr = &ti_conf_gff;

else if (strcmp(optarg, "bed") == 0) conf_ptr = &ti_conf_bed;

else if (strcmp(optarg, "sam") == 0) conf_ptr = &ti_conf_sam;

else if (strcmp(optarg, "vcf") == 0 || strcmp(optarg, "vcf4") == 0) conf_ptr = &ti_conf_vcf;

else if (strcmp(optarg, "psltbl") == 0) conf_ptr = &ti_conf_psltbl;

else {

fprintf(stderr, "[main] unrecognized preset '%s'\n", optarg);

return 1;

}

break;

case 's': conf.sc = atoi(optarg); break;

case 'b': conf.bc = atoi(optarg); break;

case 'e': conf.ec = atoi(optarg); break;

case 'l': list_chrms = 1; break;

case 'h': print_header = 1; break;

case 'H': print_only_header = 1; break;

case 'f': force = 1; break;

case 'r': reheader = optarg; break;

}

}

if (optind == argc) {

fprintf(stderr, "\n");

fprintf(stderr, "Program: tabix (TAB-delimited file InderXer)\n");

fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);

fprintf(stderr, "Usage: tabix <in.tab.bgz> [region1 [region2 [...]]]\n\n");

fprintf(stderr, "Options: -p STR preset: gff, bed, sam, vcf, psltbl [gff]\n");

fprintf(stderr, " -s INT sequence name column [1]\n");

fprintf(stderr, " -b INT start column [4]\n");

fprintf(stderr, " -e INT end column; can be identical to '-b' [5]\n");

fprintf(stderr, " -S INT skip first INT lines [0]\n");

fprintf(stderr, " -c CHAR symbol for comment/meta lines [#]\n");

fprintf(stderr, " -r FILE replace the header with the content of FILE [null]\n");

fprintf(stderr, " -B region1 is a BED file (entire file will be read)\n");

fprintf(stderr, " -0 zero-based coordinate\n");

fprintf(stderr, " -h print also the header lines\n");

fprintf(stderr, " -H print only the header lines\n");

fprintf(stderr, " -l list chromosome names\n");

fprintf(stderr, " -f force to overwrite the index\n");

fprintf(stderr, "\n");

return 1;

}

if ( !conf_ptr )

{

int l = strlen(argv[optind]);

//int strcasecmp(const char *s1, const char *s2);

if (l>=7 && strcasecmp(argv[optind]+l-7, ".gff.gz") == 0) conf_ptr = &ti_conf_gff;

else if (l>=7 && strcasecmp(argv[optind]+l-7, ".bed.gz") == 0) conf_ptr = &ti_conf_bed;

else if (l>=7 && strcasecmp(argv[optind]+l-7, ".sam.gz") == 0) conf_ptr = &ti_conf_sam;

else if (l>=7 && strcasecmp(argv[optind]+l-7, ".vcf.gz") == 0) conf_ptr = &ti_conf_vcf;

else if (l>=10 && strcasecmp(argv[optind]+l-10, ".psltbl.gz") == 0) conf_ptr = &ti_conf_psltbl;

}

if ( conf_ptr )

conf = *conf_ptr;

if (skip >= 0) conf.line_skip = skip;

if (meta >= 0) conf.meta_char = meta;

if (list_chrms) {

ti_index_t *idx;

int i, n;

const char **names;

idx = ti_index_load(argv[optind]);

if (idx == 0) {

fprintf(stderr, "[main] fail to load the index file.\n");

return 1;

}

names = ti_seqname(idx, &n);

for (i = 0; i < n; ++i) printf("%s\n", names[i]);

free(names);

ti_index_destroy(idx);

return 0;

}

if (reheader)

return reheader_file(reheader,argv[optind],conf.meta_char);

fnidx = calloc(strlen(argv[optind]) + 5, 1);

strcat(strcpy(fnidx, argv[optind]), ".tbi");

if (optind + 1 == argc && !print_only_header) {

if (force == 0) {

if (_stat64(fnidx, &stat_tbi) == 0)

{

// Before complaining, check if the VCF file isn't newer. This is a common source of errors,

// people tend not to notice that tabix failed

_stat64(argv[optind], &stat_vcf);

if ( stat_vcf.st_mtime <= stat_tbi.st_mtime )

{

fprintf(stderr, "[tabix] the index file exists. Please use '-f' to overwrite.\n");

free(fnidx);

return 1;

}

}

}

if ( bgzf_is_bgzf(argv[optind])!=1 )

{

fprintf(stderr,"[tabix] was bgzip used to compress this file? %s\n", argv[optind]);

free(fnidx);

return 1;

}

if ( !conf_ptr )

{

// Building the index but the file type was neither recognised nor given. If no custom change

// has been made, warn the user that GFF is used

if ( conf.preset==ti_conf_gff.preset

&& conf.sc==ti_conf_gff.sc

&& conf.bc==ti_conf_gff.bc

&& conf.ec==ti_conf_gff.ec

&& conf.meta_char==ti_conf_gff.meta_char

&& conf.line_skip==ti_conf_gff.line_skip )

fprintf(stderr,"[tabix] The file type not recognised and -p not given, using the preset [gff].\n");

}

return ti_index_build(argv[optind], &conf);

}

{ // retrieve

tabix_t *t;

// On some systems, stat on non-existent files returns undefined value for sm_mtime, the user had to use -f

int is_remote = (strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx) ? 1 : 0;

if ( !is_remote )

{

// Common source of errors: new VCF is used with an old index

_stat64(fnidx, &stat_tbi);

_stat64(argv[optind], &stat_vcf);

if ( force==0 && stat_vcf.st_mtime > stat_tbi.st_mtime )

{

fprintf(stderr, "[tabix] the index file either does not exist or is older than the vcf file. Please reindex.\n");

free(fnidx);

return 1;

}

}

free(fnidx);

if ((t = ti_open(argv[optind], 0)) == 0) {

fprintf(stderr, "[main] fail to open the data file.\n");

return 1;

}

if ( print_only_header )

{

ti_iter_t iter;

const char *s;

int len;

const ti_conf_t *idxconf;

if (ti_lazy_index_load(t) < 0 && bed_reg == 0) {

fprintf(stderr,"[tabix] failed to load the index file.\n");

return 1;

}

idxconf = ti_get_conf(t->idx);

iter = ti_query(t, 0, 0, 0);

while ((s = ti_read(t, iter, &len)) != 0) {

if ((int)(*s) != idxconf->meta_char) break;

fputs(s, stdout); fputc('\n', stdout);

}

ti_iter_destroy(iter);

return 0;

}

if (strcmp(argv[optind+1], ".") == 0) { // retrieve all

ti_iter_t iter;

const char *s;

int len;

iter = ti_query(t, 0, 0, 0);

while ((s = ti_read(t, iter, &len)) != 0) {

fputs(s, stdout); fputc('\n', stdout);

}

ti_iter_destroy(iter);

} else { // retrieve from specified regions

int i, len;

ti_iter_t iter;

const char *s;

const ti_conf_t *idxconf;

if (ti_lazy_index_load(t) < 0 && bed_reg == 0) {

fprintf(stderr,"[tabix] failed to load the index file.\n");

return 1;

}

idxconf = ti_get_conf(t->idx);

if ( print_header )

{

// If requested, print the header lines here

iter = ti_query(t, 0, 0, 0);

while ((s = ti_read(t, iter, &len)) != 0) {

if ((int)(*s) != idxconf->meta_char) break;

fputs(s, stdout); fputc('\n', stdout);

}

ti_iter_destroy(iter);

}

if (bed_reg) {

extern int bed_overlap(const void *_h, const char *chr, int beg, int end);

extern void *bed_read(const char *fn);

extern void bed_destroy(void *_h);

const ti_conf_t *conf_ = idxconf? idxconf : &conf; // use the index file if available

void *bed = bed_read(argv[optind+1]); // load the BED file

ti_interval_t intv;

if (bed == 0) {

fprintf(stderr, "[main] fail to read the BED file.\n");

return 1;

}

iter = ti_query(t, 0, 0, 0);

while ((s = ti_read(t, iter, &len)) != 0) {

int c;

ti_get_intv(conf_, len, (char*)s, &intv);

c = *intv.se; *intv.se = '\0';

if (bed_overlap(bed, intv.ss, intv.beg, intv.end)) {

*intv.se = c;

puts(s);

}

*intv.se = c;

}

ti_iter_destroy(iter);

bed_destroy(bed);

} else {

for (i = optind + 1; i < argc; ++i) {

int tid, beg, end;

if (ti_parse_region(t->idx, argv[i], &tid, &beg, &end) == 0) {

iter = ti_queryi(t, tid, beg, end);

while ((s = ti_read(t, iter, &len)) != 0) {

fputs(s, stdout); fputc('\n', stdout);

}

ti_iter_destroy(iter);

}

// else fprintf(stderr, "[main] invalid region: unknown target name or minus interval.\n");

}

}

}

ti_close(t);

}

return 0;

}

//Dong Code

int getpagesize()

{

SYSTEM_INFO lpSystemInfo;

GetSystemInfo(&lpSystemInfo);

return lpSystemInfo.dwPageSize;

}