static
rc_t fe_new_region(fe_context_t *self, size_t region_count, const region_t region[])
{
rc_t rc = 0;
int i;
self->region.nreads = region_count / 2;
DEBUG_MSG(3, ("REGION: %u -> %u reads\n", region_count, self->region.nreads));
if( self->region.nreads <= 0 || self->region.nreads > ABSOLID_FMT_MAX_NUM_READS ) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcUnsupported);
SRALoaderFile_LOG(self->ctx.file, klogErr, rc, "read count $(c)", PLOG_U8(c), self->region.nreads);
}
for(i = 0; rc == 0 && i < self->region.nreads ; i++ ) {
int j = i * 2 + 1;
self->region.start[i] = region[j].start;
if( (rc = set_label_type(region[j].name, &self->region.label[i], &self->region.type[i])) != 0 ) {
break;
}
self->region.cs_key[i] = region[j - 1].name[0];
DEBUG_MSG(3, ("REGION[%u]: '%s', %u, '%c', start: %u\n",
i, self->region.label[i].data, self->region.type[i], self->region.cs_key[i], self->region.start[i]));
switch(region[j].type) {
case Biological:
case Normal:
case Paired:
case Technical:
break;
default:
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcUnexpected);
SRALoaderFile_LOG(self->ctx.file, klogErr, rc, "read #$(read_id) type mismatch; expected $(expected), got $(got)",
"read_id=%u,expected=%s,got=%u", i, "(B|N|P|T)", region[j].type);
return rc;
}
}
if( rc == 0 &&
self->region.nreads > 1 && self->region.type[0] == self->region.type[1] ) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcDuplicate);
SRALoaderFile_LOG(self->ctx.file, klogErr, rc, "both reads have same type", NULL);
}
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;
}
static
rc_t parse_v1_read(SRF_context *ctx, ZTR_Context *ztr_ctx, const uint8_t *data, size_t size)
{
rc_t rc = 0;
size_t i, parsed;
ztr_raw_t ztr_raw;
ztr_t ztr;
enum ztr_chunk_type type;
fe_context_t* fe = (fe_context_t*)ctx;
uint8_t flags;
pstring readId;
EAbisolidReadType read_type;
pstring label;
AbsolidRead read[ABSOLID_FMT_MAX_NUM_READS];
if( fe->region.nreads == 0 ) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcNotFound);
return SRALoaderFile_LOG(ctx->file, klogErr, rc, "missing region chunk before 1st read chunk", NULL);
}
if( (rc = SRF_ParseReadChunk(data, size, &parsed, &flags, &readId)) != 0 ) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rc);
return SRALoaderFile_LOG(ctx->file, klogErr, rc, "SRF parsing failure", NULL);
}
ABI_ZTR_AddToBuffer(ztr_ctx, data + parsed, size - parsed);
/* readId will have spotname */
if( (rc = fe_new_read(fe, &readId, &read_type, &label)) != 0 ) {
return SRALoaderFile_LOG(ctx->file, klogErr, rc, "parsing spot name suffix", NULL);
}
for(i = 0; i < sizeof(read) / sizeof(read[0]); i++) {
AbsolidRead_Init(&read[i]);
}
while(!ABI_ZTR_BufferIsEmpty(ztr_ctx)) {
if( (rc = ABI_ZTR_ParseBlock(ztr_ctx, &ztr_raw)) != 0 ||
(rc = ABI_ZTR_ProcessBlock(ztr_ctx, &ztr_raw, &ztr, &type)) != 0 ) {
SRALoaderFile_LOG(ctx->file, klogErr, rc, "ZTR parsing failure", NULL);
break;
}
switch (type) {
case BASE:
if(ztr.sequence->datatype != i8) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcUnexpected);
SRALoaderFile_LOG(ctx->file, klogErr, rc, "read: expected 8-bit datatype", NULL);
} else if( read_type > eAbisolidReadType_SPOT ) {
int read_number = AbisolidReadType2ReadNumber[read_type];
if( (rc = pstring_assign(&read[read_number].seq, ztr.sequence->data, ztr.sequence->datasize)) == 0 ) {
/* grab 1st, may be the only cs_key */
read[read_number].cs_key = fe->region.cs_key[0];
for(i = 1; i < fe->region.nreads; i++) {
if( read_type == fe->region.type[i] ) {
read[read_number].cs_key = fe->region.cs_key[i];
break;
}
}
SRF_set_read_filter(&read[read_number].filter, flags);
rc = pstring_copy(&read[read_number].label, &label);
DEBUG_MSG(3, ("SRF READ: '%s'\n", read[read_number].seq.data));
}
if( rc != 0 ) {
SRALoaderFile_LOG(ctx->file, klogErr, rc, "copying read", NULL);
}
} else {
for(i = 0; rc == 0 && i < fe->region.nreads; i++) {
int read_number = AbisolidReadType2ReadNumber[fe->region.type[i]];
size_t len = (i + 1 >= fe->region.nreads ? ztr.sequence->datasize : fe->region.start[i + 1]) - fe->region.start[i];
rc = pstring_assign(&read[read_number].seq, &ztr.sequence->data[fe->region.start[i]], len);
read[read_number].cs_key = fe->region.cs_key[i];
SRF_set_read_filter(&read[read_number].filter, flags);
if( fe->region.label[i].len != 0 ) {
rc = pstring_copy(&read[read_number].label, &fe->region.label[i]);
}
DEBUG_MSG(3, ("SRF READ[%u]: '%s'\n", i, read[read_number].seq.data));
}
if( rc != 0 ) {
SRALoaderFile_LOG(ctx->file, klogErr, rc, "copying reads", NULL);
}
}
break;
case CNF1:
if(ztr.quality1->datatype != i8) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcUnexpected);
SRALoaderFile_LOG(ctx->file, klogErr, rc, "quality: expected 8-bit datatype", NULL);
} else if( read_type > eAbisolidReadType_SPOT ) {
int read_number = AbisolidReadType2ReadNumber[read_type];
if( (rc = pstring_assign(&read[read_number].qual, ztr.quality1->data, ztr.quality1->datasize)) == 0 ) {
DEBUG_MSG(3, ("SRF QUAL: %u bytes\n", read[read_number].qual.len));
}
if( rc != 0 ) {
SRALoaderFile_LOG(ctx->file, klogErr, rc, "copying quality", NULL);
}
} else {
for(i = 0; rc == 0 && i < fe->region.nreads; i++) {
int read_number = AbisolidReadType2ReadNumber[fe->region.type[i]];
size_t len = (i + 1 >= fe->region.nreads ? ztr.quality1->datasize : fe->region.start[i + 1]) - fe->region.start[i];
rc = pstring_assign(&read[read_number].qual, &ztr.quality1->data[fe->region.start[i]], len);
DEBUG_MSG(3, ("SRF QUAL[%u]: %u bytes\n", i, read[read_number].qual.len));
}
if( rc != 0 ) {
SRALoaderFile_LOG(ctx->file, klogErr, rc, "copying qualities", NULL);
}
}
break;
case SAMP:
if( !fe->skip_signal ) {
size_t i;
int stype = ABSOLID_FMT_COLMASK_NOTSET;
if(ztr.signal->datatype != f32) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcUnexpected);
SRALoaderFile_LOG(ctx->file, klogErr, rc, "signal: expected 32-bit float datatype", NULL);
} else if( (ztr.signal->datasize % sizeof(float)) != 0 ) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcInvalid);
SRALoaderFile_LOG(ctx->file, klogErr, rc, "signal: size not 32-bit float aligned", NULL);
} else if (ztr.signal->channel == NULL) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcIncomplete);
SRALoaderFile_LOG(ctx->file, klogErr, rc, "SIGNAL column: missing channel type", NULL);
} else if(strcmp(ztr.signal->channel, "0FAM") == 0) {
stype = ABSOLID_FMT_COLMASK_FAM;
} else if(strcmp(ztr.signal->channel, "1CY3") == 0) {
stype = ABSOLID_FMT_COLMASK_CY3;
} else if(strcmp(ztr.signal->channel, "2TXR") == 0) {
stype = ABSOLID_FMT_COLMASK_TXR;
} else if(strcmp(ztr.signal->channel, "3CY5") == 0) {
stype = ABSOLID_FMT_COLMASK_CY5;
} else {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcUnexpected);
SRALoaderFile_LOG(ctx->file, klogErr, rc, "SIGNAL column: unexpected channel type", NULL);
}
#if __BYTE_ORDER == __LITTLE_ENDIAN
for(i = 0; rc == 0 && i < ztr.signal->datasize; i += 4) {
uint32_t* r = (uint32_t*)&ztr.signal->data[i];
*r = bswap_32(*r);
}
#endif
if( rc == 0 ) {
if( read_type > eAbisolidReadType_SPOT ) {
int read_number = AbisolidReadType2ReadNumber[read_type];
pstring* d = NULL;
switch(stype) {
case ABSOLID_FMT_COLMASK_FAM:
read[read_number].fs_type = eAbisolidFSignalType_FAM;
d = &read[read_number].fxx;
break;
case ABSOLID_FMT_COLMASK_CY3:
d = &read[read_number].cy3;
break;
case ABSOLID_FMT_COLMASK_TXR:
d = &read[read_number].txr;
break;
case ABSOLID_FMT_COLMASK_CY5:
d = &read[read_number].cy5;
break;
}
if( d ) {
rc = pstring_assign(d, ztr.signal->data, ztr.signal->datasize);
DEBUG_MSG(3, ("SRF SIGNAL[%s]: %u bytes\n", ztr.signal->channel, d->len));
} else {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcUnrecognized);
}
if( rc != 0 ) {
SRALoaderFile_LOG(ctx->file, klogErr, rc, "copying signal", NULL);
}
} else {
if( fe->region.nreads <= 0 || fe->region.nreads > ABSOLID_FMT_MAX_NUM_READS ) {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcUnsupported);
SRALoaderFile_LOG(fe->ctx.file, klogErr, rc, "read count $(c)", PLOG_U8(c), fe->region.nreads);
}
for(i = 0; rc == 0 && i < fe->region.nreads; i++) {
pstring* d = NULL;
int read_number = AbisolidReadType2ReadNumber[fe->region.type[i]];
size_t len = (i + 1 >= fe->region.nreads) ? ztr.signal->datasize : (fe->region.start[i + 1] * sizeof(float));
len -= fe->region.start[i] * sizeof(float);
switch(stype) {
case ABSOLID_FMT_COLMASK_FAM:
read[read_number].fs_type = eAbisolidFSignalType_FAM;
d = &read[read_number].fxx;
break;
case ABSOLID_FMT_COLMASK_CY3:
d = &read[read_number].cy3;
break;
case ABSOLID_FMT_COLMASK_TXR:
d = &read[read_number].txr;
break;
case ABSOLID_FMT_COLMASK_CY5:
d = &read[read_number].cy5;
break;
}
if( d ) {
rc = pstring_assign(d, &ztr.signal->data[fe->region.start[i] * sizeof(float)], len);
DEBUG_MSG(3, ("SRF SIGNAL[%s]: %u bytes\n", ztr.signal->channel, d->len));
} else {
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcUnrecognized);
}
}
if( rc != 0 ) {
SRALoaderFile_LOG(ctx->file, klogErr, rc, "copying signals", NULL);
}
}
}
}
break;
default:
break;
}
if(type != none && type != ignore) {
free(*(void **)&ztr);
}
}
if(rc == 0) {
if( read_type <= eAbisolidReadType_SPOT ) {
rc = SRAWriteAbsolid_Write(fe->writer, ctx->file, &readId, NULL, &read[0], &read[1]);
} else {
switch( AbisolidReadType2ReadNumber[read_type] ) {
case 0:
rc = SRAWriteAbsolid_Write(fe->writer, ctx->file, &readId, NULL, &read[0], NULL);
break;
case 1:
rc = SRAWriteAbsolid_Write(fe->writer, ctx->file, &readId, NULL, NULL, &read[1]);
break;
default:
rc = RC(rcSRA, rcFormatter, rcParsing, rcData, rcUnsupported);
SRALoaderFile_LOG(ctx->file, klogErr, rc, "more than 2 reads", NULL);
break;
}
}
}
return rc;
}
static rc_t ReadFilterSplitter_GetKeySet( const SRASplitter* cself,
const SRASplitter_Keys** key, uint32_t* keys, spotid_t spot, const readmask_t* readmask )
{
rc_t rc = 0;
ReadFilterSplitter* self = ( ReadFilterSplitter* )cself;
if ( self == NULL || key == NULL )
{
rc = RC( rcSRA, rcNode, rcExecuting, rcParam, rcNull );
}
else
{
const INSDC_SRA_read_filter* rdf;
bitsz_t o = 0, sz = 0;
*keys = 0;
if ( self->col_rdf != NULL )
{
rc = SRAColumnRead( self->col_rdf, spot, (const void **)&rdf, &o, &sz );
if ( rc == 0 )
{
int32_t j, i = sz / sizeof( INSDC_SRA_read_filter ) / 8;
*key = self->keys;
*keys = sizeof( self->keys ) / sizeof( self->keys[ 0 ] );
for ( j = 0; j < *keys; j++ )
{
clear_readmask( self->keys[ j ].readmask );
}
while ( i > 0 )
{
i--;
if ( self->read_filter != 0xFF && self->read_filter != rdf[i] )
{
/* skip by filter value != to command line */
}
else if ( rdf[ i ] == SRA_READ_FILTER_PASS )
{
set_readmask( self->keys[ EReadFilterSplitter_pass ].readmask, i );
}
else if ( rdf[ i ] == SRA_READ_FILTER_REJECT )
{
set_readmask( self->keys[ EReadFilterSplitter_reject ].readmask, i );
}
else if( rdf[ i ] == SRA_READ_FILTER_CRITERIA )
{
set_readmask( self->keys[ EReadFilterSplitter_criteria ].readmask, i );
}
else if( rdf[ i ] == SRA_READ_FILTER_REDACTED )
{
set_readmask( self->keys[ EReadFilterSplitter_redacted ].readmask, i );
}
else
{
set_readmask( self->keys[ EReadFilterSplitter_unknown ].readmask, i );
PLOGMSG( klogWarn, ( klogWarn,
"unknown READ_FILTER value $(value) at spot id $(row)",
PLOG_2( PLOG_U8( value ), PLOG_I64( row ) ), rdf[ i ], spot ) );
}
}
}
}
}
return rc;
}
