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;
}
rc_t SFFLoaderFmtMake(SRALoaderFmt** self, const SRALoaderConfig* config)
{
rc_t rc = 0;
SFFLoaderFmt* obj = NULL;
const PlatformXML* platform;
if( self == NULL || config == NULL ) {
return RC(rcSRA, rcFormatter, rcConstructing, rcSelf, rcNull);
}
*self = NULL;
if( (rc = Experiment_GetPlatform(config->experiment, &platform)) != 0 ) {
return rc;
}
obj = calloc(1, sizeof(SFFLoaderFmt));
if(obj == NULL) {
return RC(rcSRA, rcFormatter, rcConstructing, rcMemory, rcExhausted);
}
if( (rc = SRALoaderFmtInit(&obj->dad, (const SRALoaderFmt_vt*)&vtSFFLoaderFmt)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize parent object");
} else {
if( platform->id == SRA_PLATFORM_454 ) {
if( (rc = SRAWriter454_Make(&obj->w454, config)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize writer");
}
} else {
if( (rc = SRAWriterIonTorrent_Make(&obj->wIonTorrent, config)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize Ion Torrent writer");
}
}
}
if(rc == 0) {
obj->skip_signal = (config->columnFilter & efltrSIGNAL) && !(config->columnFilter & efltrDEFAULT);
*self = &obj->dad;
} else {
free(obj);
}
return rc;
}
rc_t SRAWriterIllumina_Make(const SRAWriterIllumina** cself, const SRALoaderConfig* config)
{
rc_t rc = 0;
SRAWriterIllumina* self;
const PlatformXML* platform;
const ReadSpecXML_read* last_read;
int32_t spot_len;
uint32_t sequence_length;
uint8_t nreads;
if( cself == NULL || config == NULL ) {
return RC(rcSRA, rcFormatter, rcConstructing, rcParam, rcNull);
}
if( (rc = Experiment_GetPlatform(config->experiment, &platform)) != 0 ||
(rc = Experiment_GetReadNumber(config->experiment, &nreads)) != 0 ||
(rc = Experiment_GetSpotLength(config->experiment, &sequence_length)) != 0 ||
(rc = Experiment_GetRead(config->experiment, nreads - 1, &last_read)) != 0 ) {
return rc;
}
if( platform->id != SRA_PLATFORM_ILLUMINA ) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcData, rcInvalid);
LOGERR(klogErr, rc, "platform type");
return rc;
}
if( nreads > ILLUMINAWRITER_MAX_NUM_READS ) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcData, rcUnsupported);
PLOGERR(klogErr, (klogErr, rc, "more than $(max) reads", PLOG_U8(max), (uint8_t)ILLUMINAWRITER_MAX_NUM_READS));
return rc;
}
self = calloc(1, sizeof(*self));
if( self == NULL ) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcMemory, rcExhausted);
return rc;
}
if( (rc = SRAWriter_Make(&self->base, config)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize base writer");
}
self->config = config;
self->platform = platform;
self->nreads = nreads;
self->barcode_read_id = ILLUMINAWRITER_READID_NONE;
self->last_read = last_read;
self->fixed_read_seg = true;
self->col_mask = ILLUMINAWRITER_COLMASK_NOTSET;
self->sequence_length = sequence_length;
spot_len = sequence_length;
do {
const ReadSpecXML_read* read_spec;
int16_t len = 0;
--nreads;
if( (rc = Experiment_GetRead(config->experiment, nreads, &read_spec)) != 0 ) {
break;
}
if( read_spec->read_type == rdsp_BarCode_rt ) {
if( self->barcode_read_id == ILLUMINAWRITER_READID_NONE ) {
self->barcode_read_id = nreads;
} else {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcData, rcDuplicate);
LOGERR(klogErr, rc, "only on BarCode READ_TYPE per spot supported");
break;
}
}
if( self->fixed_read_seg ) {
switch(read_spec->coord_type) {
case rdsp_BaseCoord_ct:
case rdsp_CycleCoord_ct:
len = spot_len - read_spec->coord.start_coord + 1;
break;
case rdsp_ExpectedBaseCall_ct:
case rdsp_ExpectedBaseCallTable_ct:
if( read_spec->coord.expected_basecalls.default_length > 0 ) {
len = read_spec->coord.expected_basecalls.default_length;
} else {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcData, rcUnsupported);
}
break;
case rdsp_RelativeOrder_ct:
if( nreads == 0 ) {
len = spot_len - 1 + 1; /* as if BASE_COORD == 1 */
break;
}
default:
rc = RC(rcSRA, rcFormatter, rcConstructing, rcData, rcUnsupported);
}
if( rc == 0 ) {
spot_len -= len;
if( spot_len < 0 || len <= 0 ) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcData, rcInconsistent);
LOGERR(klogErr, rc, "SPOT_DECODE_SPEC and SEQUENCE_LENGTH");
} else {
SRASegment* seg = &self->read_seg[nreads];
seg->start = spot_len;
seg->len = len;
DEBUG_MSG(3, ("#%u read fixed length = %i\n", nreads, len));
}
} else if( GetRCState(rc) == rcUnsupported ) {
self->fixed_read_seg = false;
DEBUG_MSG(3, ("not fixed spot segmentation"));
rc = 0;
}
}
} while( rc == 0 && nreads > 0 );
if( rc == 0 ) {
*cself = self;
} else {
SRAWriterIllumina_Whack(self, NULL);
}
return rc;
}
rc_t SRAWriteAbsolid_Make(const SRAWriteAbsolid** cself, const SRALoaderConfig* config)
{
rc_t rc = 0;
SRAWriteAbsolid* self;
const PlatformXML* platform;
const ReadSpecXML_read* read;
uint32_t sequence_length;
uint8_t nreads;
if( cself == NULL || config == NULL ) {
return RC(rcSRA, rcFormatter, rcConstructing, rcParam, rcNull);
}
if( (rc = Experiment_GetPlatform(config->experiment, &platform)) != 0 ||
(rc = Experiment_GetSpotLength(config->experiment, &sequence_length)) != 0 ||
(rc = Experiment_GetReadNumber(config->experiment, &nreads)) != 0 ) {
return rc;
}
if( platform->id != SRA_PLATFORM_ABSOLID ) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcInvalid);
LOGERR(klogErr, rc, "platform type");
return rc;
}
if( nreads > ABSOLID_FMT_MAX_NUM_READS ) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcData, rcUnsupported);
PLOGERR(klogErr, (klogErr, rc, "expected up to $(max) reads", "max=%u", ABSOLID_FMT_MAX_NUM_READS));
return rc;
}
self = calloc(1, sizeof(*self));
if( self == NULL ) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcMemory, rcExhausted);
return rc;
}
if( (rc = SRAWriter_Make(&self->base, config)) != 0 ) {
LOGERR(klogInt, rc, "failed to initialize base writer");
} else if( (rc = Experiment_GetRead(config->experiment, 0, &read)) != 0 ) {
LOGERR(klogInt, rc, "failed to get read 1 descriptor");
} else if( read->coord_type != rdsp_RelativeOrder_ct && read->coord_type != rdsp_BaseCoord_ct ) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcData, rcInvalid);
LOGERR(klogErr, rc, "1st read can be BASE_COORD or RELATIVE_ORDER only");
} else if( read->read_type != rdsp_Forward_rt && read->read_type != rdsp_Reverse_rt ) {
LOGMSG(klogWarn, "expected 1st read to be of type 'Forward' or 'Reverse'");
}
self->read_seg[0].start = 0;
self->read_seg[0].len = sequence_length;
if( rc == 0 && nreads >= ABSOLID_FMT_MAX_NUM_READS ) {
if( nreads > ABSOLID_FMT_MAX_NUM_READS ) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcData, rcUnsupported);
LOGERR(klogErr, rc, "more than 2 reads");
} else if( (rc = Experiment_GetRead(config->experiment, 1, &read)) != 0 ) {
LOGERR(klogErr, rc, "failed to get read 2 descriptor");
} else if( read->coord_type != rdsp_BaseCoord_ct ) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcData, rcInvalid);
LOGERR(klogErr, rc, "2nd read can be BASE_COORD only");
} else if( read->read_type != rdsp_Forward_rt && read->read_type != rdsp_Reverse_rt ) {
LOGMSG(klogWarn, "expected 2ndt read to be of type 'Forward' or 'Reverse'");
}
if( rc == 0 ) {
self->read_seg[1].start = read->coord.start_coord - 1;
self->read_seg[1].len = sequence_length - self->read_seg[1].start;
self->read_seg[0].len = self->read_seg[1].start;
}
}
#if _DEBUGGING
DEBUG_MSG(3, ("%s READ_SEG[%hu,%hu]\n", __func__, self->read_seg[0].start, self->read_seg[0].len));
if( nreads > 1 ) {
DEBUG_MSG(3, ("%s READ_SEG[%hu,%hu]\n", __func__, self->read_seg[1].start, self->read_seg[1].len));
}
#endif
if( rc == 0 ) {
self->platform = platform;
self->nreads = nreads;
*cself = self;
} else {
SRAWriteAbsolid_Whack(self, NULL);
}
return rc;
}
