static rc_t fe_new_read(fe_context_t *self, int flags, pstring *readId ) { rc_t rc; char *suffix; pstring readName, spotGroup; static IlluminaSpot spot; /* look for spot group */ suffix = strchr(readId->data, '#'); if( suffix != NULL ) { readId->len = suffix++ - readId->data; if( (rc = pstring_assign(&spotGroup, suffix, strlen(suffix))) != 0 ) { SRALoaderFile_LOG(self->ctx.file, klogInt, rc, "extracting barcode from spot '$(spotname)'", "spotname=%s", readId->data); return rc; } } else { pstring_clear(&spotGroup); } /* build the read name from prefix (self->name_prefix) and read id */ if(self->name_prefix.len > 0 ) { if( (rc = pstring_copy(&readName, &self->name_prefix)) == 0 ) { if( isdigit(readName.data[readName.len - 1]) ) { rc = pstring_append(&readName, ":", 1); } if( rc == 0 ) { rc = pstring_concat(&readName, readId); } } } else { rc = pstring_copy(&readName, readId); } if( rc != 0 ) { SRALoaderFile_LOG(self->ctx.file, klogErr, rc, "preparing spot name $(spotname)", "spotname=%s", readId->data); return rc; } SRF_set_read_filter(&self->read.filter, flags); IlluminaSpot_Init(&spot); if( (rc = IlluminaSpot_Add(&spot, &readName, &spotGroup, &self->read)) == 0 ) { rc = SRAWriterIllumina_Write(self->writer, self->ctx.file, &spot); } 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; }