WiggleIterator * BamReader(char * filename, bool holdFire) {
BamReaderData * data = (BamReaderData *) calloc(1, sizeof(BamReaderData));
setSamtoolsDefaultConf(data);
OpenBamFile(data, filename);
if (!holdFire)
launchBufferedReader(&downloadBamFile, data, &(data->bufferedReaderData));
return newWiggleIterator(data, &BamReaderPop, &BamReaderSeek, 0);
}
void openBigBed(BigBedReaderData * data, char * filename, bool holdFire) {
if(!bbIsBigBed(filename, NULL)) {
printf("File %s is not in BigBed format", filename);
exit(1);
}
data->fp = bbOpen(filename, NULL);
if (!holdFire)
launchBufferedReader(&readBigBed, data, &(data->bufferedReaderData));
}
void BcfReaderSeek(WiggleIterator * wi, const char * chrom, int start, int finish) {
BCFReaderData * data = (BCFReaderData *) wi->data;
killBufferedReader(data->bufferedReaderData);
data->tabix_iterator = ti_query(data->tabix_file, chrom, start, finish);
launchBufferedReader(&downloadTabixFile, data, &(data->bufferedReaderData));
wi->done = false;
BCFReaderPop(wi);
while (!wi->done && (strcmp(wi->chrom, chrom) < 0 || (strcmp(chrom, wi->chrom) == 0 && wi->finish <= start)))
BCFReaderPop(wi);
data->chrom = chrom;
data->stop = finish;
}
void BigBedReaderSeek(WiggleIterator * wi, const char * chrom, int start, int finish) {
BigBedReaderData * data = (BigBedReaderData *) wi->data;
if (data->bufferedReaderData) {
killBufferedReader(data->bufferedReaderData);
free(data->bufferedReaderData);
data->bufferedReaderData = NULL;
}
data->chrom = chrom;
data->start = start;
data->stop = finish;
launchBufferedReader(&readBigBed, data, &(data->bufferedReaderData));
wi->done = false;
BigBedReaderPop(wi);
while (!wi->done && (strcmp(wi->chrom, chrom) < 0 || (strcmp(chrom, wi->chrom) == 0 && wi->finish <= start)))
BigBedReaderPop(wi);
if (!wi->done && strcmp(chrom, wi->chrom) == 0 && wi->start < start)
wi->start = start;
}
void BamReaderSeek(WiggleIterator * wi, const char * chrom, int start, int finish) {
BamReaderData * data = (BamReaderData *) wi->data;
char region[1000];
if (data->bufferedReaderData) {
killBufferedReader(data->bufferedReaderData);
free(data->bufferedReaderData);
data->bufferedReaderData = NULL;
}
data->chrom = chrom;
data->stop = finish;
sprintf(region, "%s:%i-%i", chrom, start, finish);
data->conf->reg = region;
seekRegion(data);
launchBufferedReader(&downloadBamFile, data, &(data->bufferedReaderData));
wi->done = false;
BamReaderPop(wi);
while (!wi->done && (strcmp(wi->chrom, chrom) < 0 || (strcmp(wi->chrom, chrom) == 0 && wi->finish <= start)))
BamReaderPop(wi);
}
WiggleIterator * BcfReader(char * filename) {
BCFReaderData * data = (BCFReaderData *) calloc(1, sizeof(BCFReaderData));
OpenTabixFile(data, filename);
launchBufferedReader(&downloadTabixFile, data, &(data->bufferedReaderData));
return newWiggleIterator(data, &BCFReaderPop, &BcfReaderSeek);
}
