rc_t SRALoaderFmtMake(SRALoaderFmt **self, const SRALoaderConfig *config)
{
rc_t rc = 0;
IlluminaLoaderFmt* fmt;
if( self == NULL || config == NULL ) {
return RC(rcSRA, rcFormatter, rcConstructing, rcParam, rcNull);
}
*self = NULL;
fmt = calloc(1, sizeof(*fmt));
if(fmt == NULL) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcMemory, rcExhausted);
LOGERR(klogInt, rc, "failed to initialize; out of memory");
return rc;
}
if( (rc = SRAWriterIllumina_Make(&fmt->writer, config)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize writer");
} else if( (rc = SRALoaderFmtInit(&fmt->dad, (const SRALoaderFmt_vt*)&vtIlluminaLoaderFmt)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize parent object");
}
if( rc != 0 ) {
IlluminaLoaderFmt_Whack(fmt, NULL);
} else {
fmt->skip_signal = (config->columnFilter & (efltrSIGNAL | efltrDEFAULT));
fmt->skip_noise = (config->columnFilter & (efltrNOISE | efltrDEFAULT));
fmt->skip_intensity = (config->columnFilter & (efltrINTENSITY | efltrDEFAULT));
fmt->spots_bad_allowed = config->spots_bad_allowed;
fmt->spots_bad_count = 0;
*self = &fmt->dad;
}
return rc;
}
rc_t SRFIlluminaLoaderFmt_Init(SRFIlluminaLoaderFmt* self, const SRALoaderConfig* config)
{
rc_t rc = 0;
self->fe.skip_signal = (config->columnFilter & (efltrSIGNAL | efltrDEFAULT));
self->fe.skip_noise = (config->columnFilter & (efltrNOISE | efltrDEFAULT));
self->fe.skip_intensity = (config->columnFilter & (efltrINTENSITY | efltrDEFAULT));
if( (rc = SRAWriterIllumina_Make(&self->fe.writer, config)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize writer");
}
return rc;
}
rc_t SRALoaderFmtMake(SRALoaderFmt **self, const SRALoaderConfig *config)
{
rc_t rc = 0;
FastqLoaderFmt* fmt;
const PlatformXML* platform;
const ProcessingXML* processing;
if( self == NULL || config == NULL ) {
return RC(rcSRA, rcFormatter, rcConstructing, rcParam, rcNull);
}
*self = NULL;
if( (rc = Experiment_GetProcessing(config->experiment, &processing)) != 0 ||
(rc = Experiment_GetPlatform(config->experiment, &platform)) != 0 ) {
return rc;
}
fmt = calloc(1, sizeof(*fmt));
if(fmt == NULL) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcMemory, rcExhausted);
LOGERR(klogInt, rc, "failed to initialize; out of memory");
return rc;
}
if( platform->id == SRA_PLATFORM_454 ) {
if( rc == 0 && (rc = SRAWriter454_Make(&fmt->w454, config)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize 454 writer");
}
} else if( platform->id == SRA_PLATFORM_ION_TORRENT ) {
if( rc == 0 && (rc = SRAWriterIonTorrent_Make(&fmt->wIonTorrent, config)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize Ion Torrent writer");
}
} else if( (rc = SRAWriterIllumina_Make(&fmt->wIllumina, config)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize Illumina writer");
}
if( rc == 0 && (rc = SRALoaderFmtInit(&fmt->dad, (const SRALoaderFmt_vt*)&vtFastqLoaderFmt)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize parent object");
}
if( rc != 0 ) {
FastqLoaderFmt_Whack(fmt, NULL);
} else {
fmt->processing = processing;
fmt->spots_bad_allowed = config->spots_bad_allowed;
fmt->spots_bad_count = 0;
*self = &fmt->dad;
}
return rc;
}
