bool
tabix_streamer::
next() {
if (_is_stream_end || (NULL==_tfp) || (NULL==_titer)) return false;
int len;
_linebuf = (char*) ti_read(_tfp, _titer, &len);
_is_stream_end=(NULL == _linebuf);
_is_record_set=(! _is_stream_end);
if (_is_record_set) _record_no++;
return _is_record_set;
}
static PyObject *
tabixiter_iternext(TabixIteratorObject *self)
{
const char *chunk;
int len, i;
chunk = ti_read(self->tbobj->tb, self->iter, &len);
if (chunk != NULL) {
PyObject *ret, *column;
Py_ssize_t colidx;
const char *ptr, *begin;
ret = PyList_New(0);
if (ret == NULL)
return NULL;
colidx = 0;
ptr = begin = chunk;
for (i = len; i > 0; i--, ptr++)
if (*ptr == '\t') {
column = PYOBJECT_FROM_STRING_AND_SIZE(begin,
(Py_ssize_t)(ptr - begin));
if (column == NULL || PyList_Append(ret, column) == -1) {
Py_DECREF(ret);
return NULL;
}
Py_DECREF(column);
begin = ptr + 1;
colidx++;
}
column = PYOBJECT_FROM_STRING_AND_SIZE(begin, (Py_ssize_t)(ptr - begin));
if (column == NULL || PyList_Append(ret, column) == -1) {
Py_DECREF(ret);
return NULL;
}
Py_DECREF(column);
return ret;
}
else
return NULL;
}
bool
tabix_header_streamer::
next() {
if (_is_stream_end || (NULL==_tfp) || (NULL==_titer)) return false;
int len;
_linebuf = (char*) ti_read(_tfp, _titer, &len);
if (NULL == _linebuf) {
_is_stream_end=true;
} else {
if ((strlen(_linebuf)<1) || (_linebuf[0] != '#')) {
_is_stream_end=true;
}
}
_is_record_set=(! _is_stream_end);
return _is_record_set;
}
int main(int argc, char *argv[])
{
int c, skip = -1, meta = -1, list_chrms = 0, force = 0, print_header = 0, bed_reg = 0;
ti_conf_t conf = ti_conf_gff;
const char *reheader = NULL;
while ((c = getopt(argc, argv, "p:s:b:e:0S:c:lhfBr:")) >= 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 = ti_conf_gff;
else if (strcmp(optarg, "bed") == 0) conf = ti_conf_bed;
else if (strcmp(optarg, "sam") == 0) conf = ti_conf_sam;
else if (strcmp(optarg, "vcf") == 0 || strcmp(optarg, "vcf4") == 0) conf = ti_conf_vcf;
else if (strcmp(optarg, "psltbl") == 0) conf = 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 'f': force = 1; break;
case 'r': reheader = optarg; break;
}
}
if (skip >= 0) conf.line_skip = skip;
if (meta >= 0) conf.meta_char = meta;
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 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 (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);
struct stat stat_tbi,stat_vcf;
char *fnidx = calloc(strlen(argv[optind]) + 5, 1);
strcat(strcpy(fnidx, argv[optind]), ".tbi");
if (optind + 1 == argc) {
if (force == 0) {
if (stat(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
stat(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_check_bgzf(argv[optind])!=1 )
{
fprintf(stderr,"[tabix] was bgzip used to compress this file? %s\n", argv[optind]);
free(fnidx);
return 1;
}
return ti_index_build(argv[optind], &conf);
}
{ // retrieve
tabix_t *t;
// Common source of errors: new VCF is used with an old index
stat(fnidx, &stat_tbi);
stat(argv[optind], &stat_vcf);
if ( force==0 && stat_vcf.st_mtime > stat_tbi.st_mtime )
{
fprintf(stderr, "[tabix] the index file is older than the vcf file. Please use '-f' to overwrite or 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 (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;
}
static char * nextLine(BCFReaderData * data) {
if (data->tabix_iterator)
return ti_read(data->tabix_file, data->tabix_iterator, 0);
else
return gzgets(data->gz_file, data->buffer, BUFF_LENGTH);
}
boolean lineFileNext(struct lineFile *lf, char **retStart, int *retSize)
/* Fetch next line from file. */
{
char *buf = lf->buf;
int bytesInBuf = lf->bytesInBuf;
int endIx = lf->lineEnd;
boolean gotLf = FALSE;
int newStart;
if (lf->reuse)
{
lf->reuse = FALSE;
if (retSize != NULL)
*retSize = lf->lineEnd - lf->lineStart;
*retStart = buf + lf->lineStart;
if (lf->metaOutput && *retStart[0] == '#')
metaDataAdd(lf, *retStart);
return TRUE;
}
#ifdef USE_TABIX
if (lf->tabix != NULL && lf->tabixIter != NULL)
{
// Just use line-oriented ti_read:
int lineSize = 0;
const char *line = ti_read(lf->tabix, lf->tabixIter, &lineSize);
if (line == NULL)
return FALSE;
lf->bufOffsetInFile = -1;
lf->bytesInBuf = lineSize;
lf->lineIx = -1;
lf->lineStart = 0;
lf->lineEnd = lineSize;
if (lineSize > lf->bufSize)
// shouldn't be! but just in case:
lineFileExpandBuf(lf, lineSize * 2);
safecpy(lf->buf, lf->bufSize, line);
*retStart = lf->buf;
if (retSize != NULL)
*retSize = lineSize;
return TRUE;
}
#endif // USE_TABIX
determineNlType(lf, buf+endIx, bytesInBuf);
/* Find next end of line in buffer. */
switch(lf->nlType)
{
case nlt_unix:
case nlt_dos:
for (endIx = lf->lineEnd; endIx < bytesInBuf; ++endIx)
{
if (buf[endIx] == '\n')
{
gotLf = TRUE;
endIx += 1;
break;
}
}
break;
case nlt_mac:
for (endIx = lf->lineEnd; endIx < bytesInBuf; ++endIx)
{
if (buf[endIx] == '\r')
{
gotLf = TRUE;
endIx += 1;
break;
}
}
break;
case nlt_undet:
break;
}
/* If not in buffer read in a new buffer's worth. */
while (!gotLf)
{
int oldEnd = lf->lineEnd;
int sizeLeft = bytesInBuf - oldEnd;
int bufSize = lf->bufSize;
int readSize = bufSize - sizeLeft;
if (oldEnd > 0 && sizeLeft > 0)
{
memmove(buf, buf+oldEnd, sizeLeft);
}
lf->bufOffsetInFile += oldEnd;
if (lf->fd >= 0)
readSize = lineFileLongNetRead(lf->fd, buf+sizeLeft, readSize);
#ifdef USE_TABIX
else if (lf->tabix != NULL && readSize > 0)
{
readSize = ti_bgzf_read(lf->tabix->fp, buf+sizeLeft, readSize);
if (readSize < 1)
return FALSE;
}
#endif // USE_TABIX
else
readSize = 0;
if ((readSize == 0) && (endIx > oldEnd))
{
endIx = sizeLeft;
buf[endIx] = 0;
lf->bytesInBuf = newStart = lf->lineStart = 0;
lf->lineEnd = endIx;
++lf->lineIx;
if (retSize != NULL)
*retSize = endIx - newStart;
*retStart = buf + newStart;
if (*retStart[0] == '#')
metaDataAdd(lf, *retStart);
return TRUE;
}
else if (readSize <= 0)
{
lf->bytesInBuf = lf->lineStart = lf->lineEnd = 0;
return FALSE;
}
bytesInBuf = lf->bytesInBuf = readSize + sizeLeft;
lf->lineEnd = 0;
determineNlType(lf, buf+endIx, bytesInBuf);
/* Look for next end of line. */
switch(lf->nlType)
{
case nlt_unix:
case nlt_dos:
for (endIx = sizeLeft; endIx <bytesInBuf; ++endIx)
{
if (buf[endIx] == '\n')
{
endIx += 1;
gotLf = TRUE;
break;
}
}
break;
case nlt_mac:
for (endIx = sizeLeft; endIx <bytesInBuf; ++endIx)
{
if (buf[endIx] == '\r')
{
endIx += 1;
gotLf = TRUE;
break;
}
}
break;
case nlt_undet:
break;
}
if (!gotLf && bytesInBuf == lf->bufSize)
{
if (bufSize >= 512*1024*1024)
{
errAbort("Line too long (more than %d chars) line %d of %s",
lf->bufSize, lf->lineIx+1, lf->fileName);
}
else
{
lineFileExpandBuf(lf, bufSize*2);
buf = lf->buf;
}
}
}
if (lf->zTerm)
{
buf[endIx-1] = 0;
if ((lf->nlType == nlt_dos) && (buf[endIx-2]=='\r'))
{
buf[endIx-2] = 0;
}
}
lf->lineStart = newStart = lf->lineEnd;
lf->lineEnd = endIx;
++lf->lineIx;
if (retSize != NULL)
*retSize = endIx - newStart;
*retStart = buf + newStart;
if (*retStart[0] == '#')
metaDataAdd(lf, *retStart);
return TRUE;
}
