static void cvt_string(nvlist_t *nvl, nvpair_t *pair, data_type_t tgt) { const char *name = nvpair_name(pair); uint64_t intval; char *str; int ret; ASSERT3U(nvpair_type(pair), ==, DATA_TYPE_STRING); ret = nvpair_value_string(pair, &str); if (ret) return; switch (tgt) { case DATA_TYPE_UINT64: ret = str2u64(str, &intval); if (!ret) nvl_set_int(nvl, name, intval); break; default: panic("unexpected target type"); } }
static rc_t CC CGReads15_Header(const CGReads15* cself, const char* buf, const size_t len) { rc_t rc = 0; size_t slen; CGReads15* self = (CGReads15*)cself; if( strncmp("ASSEMBLY_ID\t", buf, slen = 12) == 0 ) { rc = str2buf(&buf[slen], len - slen, self->assembly_id, sizeof(self->assembly_id)); } else if( strncmp("BATCH_FILE_NUMBER\t", buf, slen = 18) == 0 ) { rc = str2u32(&buf[slen], len - slen, &self->batch_file_number); if( self->batch_file_number < 1 ) { rc = RC(rcRuntime, rcFile, rcConstructing, rcItem, rcOutofrange); } } else if( strncmp("BATCH_OFFSET\t", buf, slen = 13) == 0 ) { rc = str2u64(&buf[slen], len - slen, &self->batch_offset); } else if( strncmp("FIELD_SIZE\t", buf, slen = 11) == 0 ) { rc = str2u32(&buf[slen], len - slen, &self->field_size); } else if( strncmp("GENERATED_AT\t", buf, slen = 13) == 0 ) { rc = str2buf(&buf[slen], len - slen, self->generated_at, sizeof(self->generated_at)); } else if( strncmp("GENERATED_BY\t", buf, slen = 13) == 0 ) { rc = str2buf(&buf[slen], len - slen, self->generated_by, sizeof(self->generated_by)); } else if( strncmp("LANE\t", buf, slen = 5) == 0 ) { rc = str2buf(&buf[slen], len - slen, self->lane, sizeof(self->lane)); } else if( strncmp("LIBRARY\t", buf, slen = 8) == 0 ) { rc = str2buf(&buf[slen], len - slen, self->library, sizeof(self->library)); } else if( strncmp("SAMPLE\t", buf, slen = 7) == 0 ) { rc = str2buf(&buf[slen], len - slen, self->sample, sizeof(self->sample)); } else if( strncmp("SLIDE\t", buf, slen = 6) == 0 ) { rc = str2buf(&buf[slen], len - slen, self->slide, sizeof(self->slide)); } else if( strncmp("SOFTWARE_VERSION\t", buf, slen = 17) == 0 ) { rc = str2buf(&buf[slen], len - slen, self->software_version, sizeof(self->software_version)); } else { rc = RC(rcRuntime, rcFile, rcConstructing, rcName, rcUnrecognized); } return rc; }
static rc_t CC CGReads25_Header(const CGReads15* cself, const char* buf, const size_t len) { rc_t rc = 0; size_t slen = 0; CGReads15* self = (CGReads15*)cself; /* from SRA-2617 files */ if (strncmp("APPROVAL\t", buf, slen = 9) == 0) { } else if (strncmp("TITLE\t", buf, slen = 6) == 0) { } else if (strncmp("ADDRESS\t", buf, slen = 8) == 0) { } /* From Table 1: Header Metadata Present in all Data Files */ else if (strncmp("CUSTOMER_SAMPLE_ID\t", buf, slen = 19) == 0) { } else if (strncmp("SAMPLE_SOURCE\t", buf, slen = 14) == 0) { } else if (strncmp("REPORTED_GENDER\t", buf, slen = 16) == 0) { } else if (strncmp("CALLED_GENDER\t", buf, slen = 14) == 0) { } else if (strncmp("TUMOR_STATUS\t", buf, slen = 13) == 0) { } else if (strncmp("LIBRARY_TYPE\t", buf, slen = 13) == 0) { } else if (strncmp("LIBRARY_SOURCE\t", buf, slen = 13) == 0) { } else if (strncmp("ASSEMBLY_ID\t", buf, slen = 12) == 0) { rc = str2buf(&buf[slen], len - slen, self->assembly_id, sizeof(self->assembly_id)); } else if (strncmp("BATCH_FILE_NUMBER\t", buf, slen = 18) == 0) { rc = str2u32(&buf[slen], len - slen, &self->batch_file_number); if (self->batch_file_number < 1) { rc = RC(rcRuntime, rcFile, rcConstructing, rcItem, rcOutofrange); } } else if (strncmp("BATCH_OFFSET\t", buf, slen = 13) == 0) { rc = str2u64(&buf[slen], len - slen, &self->batch_offset); } else if (strncmp("FIELD_SIZE\t", buf, slen = 11) == 0) { rc = str2u32(&buf[slen], len - slen, &self->field_size); } else if (strncmp("GENERATED_AT\t", buf, slen = 13) == 0) { rc = str2buf(&buf[slen], len - slen, self->generated_at, sizeof(self->generated_at)); } else if (strncmp("GENERATED_BY\t", buf, slen = 13) == 0) { rc = str2buf(&buf[slen], len - slen, self->generated_by, sizeof(self->generated_by)); } else if (strncmp("LANE\t", buf, slen = 5) == 0) { rc = str2buf(&buf[slen], len - slen, self->lane, sizeof(self->lane)); } else if (strncmp("LIBRARY\t", buf, slen = 8) == 0) { rc = str2buf(&buf[slen], len - slen, self->library, sizeof(self->library)); } else if (strncmp("SAMPLE\t", buf, slen = 7) == 0) { rc = str2buf(&buf[slen], len - slen, self->sample, sizeof(self->sample)); } else if (strncmp("SLIDE\t", buf, slen = 6) == 0) { rc = str2buf(&buf[slen], len - slen, self->slide, sizeof(self->slide)); } else if (strncmp("SOFTWARE_VERSION\t", buf, slen = 17) == 0) { rc = str2buf(&buf[slen], len - slen, self->software_version, sizeof(self->software_version)); } else { rc = RC(rcRuntime, rcFile, rcConstructing, rcName, rcUnrecognized); } return rc; }
static rc_t CC CGEvidenceDnbs_Read(const CGEvidenceDnbs15* cself, const char* interval_id, TEvidenceDnbsData* data, int score_allele_num) { rc_t rc = 0; TEvidenceDnbsData_dnb* m = NULL; static TEvidenceDnbsData_dnb next_rec; static char next_interval_id[32] = ""; /* local copy of unused TEvidenceDnbsData_dnb struct elements */ char reference_alignment[CG_EVDNC_ALLELE_CIGAR_LEN]; INSDC_coord_zero mate_offset_in_reference; char mate_reference_alignment[CG_EVDNC_ALLELE_CIGAR_LEN]; uint16_t score_allele[4] = {0, 0, 0, 0}; /* v1.5 has ScoreAllele[012]; v2.0 - [0123] */ char qual[CG_EVDNC_SPOT_LEN]; strcpy(data->interval_id, interval_id); data->qty = 0; /* already read one rec for this interval_id */ if( next_interval_id[0] != '\0' ) { if( strcmp(next_interval_id, interval_id) != 0 ) { /* nothing todo since next interval id is different */ return rc; } m = &data->dnbs[data->qty++]; memcpy(m, &next_rec, sizeof(next_rec)); DEBUG_MSG(10, ("%3u evidenceDnbs: '%s'\t'%s'\t'%s'\t'%s'\t%u\t%lu\t%hu\t%c\t%c\t%i\t'%.*s'" "\t%i\tnot_used\t0\tnot_used\t%c\t0\t0\t0\t'%.*s'\t'--'\n", data->qty, next_interval_id, m->chr, m->slide, m->lane, m->file_num_in_lane, m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele, m->allele_alignment_length, m->allele_alignment, m->offset_in_reference, m->mapping_quality, m->read_len, m->read)); } do { int i = 0; char tmp[2]; CG_LINE_START(cself->file, b, len, p); if( b == NULL || len == 0 ) { next_interval_id[0] = '\0'; break; /* EOF */ } if( data->qty >= data->max_qty ) { TEvidenceDnbsData_dnb* x; data->max_qty += 100; x = realloc(data->dnbs, sizeof(*(data->dnbs)) * data->max_qty); if( x == NULL ) { rc = RC(rcRuntime, rcFile, rcReading, rcMemory, rcExhausted); break; } data->dnbs = x; } m = &data->dnbs[data->qty++]; /*DEBUG_MSG(10, ("%2hu evidenceDnbs: '%.*s'\n", data->qty, len, b));*/ CG_LINE_NEXT_FIELD(b, len, p); rc = str2buf(b, p - b, next_interval_id, sizeof(next_interval_id)); CG_LINE_NEXT_FIELD(b, len, p); rc = str2buf(b, p - b, m->chr, sizeof(m->chr)); CG_LINE_NEXT_FIELD(b, len, p); rc = str2buf(b, p - b, m->slide, sizeof(m->slide)); CG_LINE_NEXT_FIELD(b, len, p); rc = str2buf(b, p - b, m->lane, sizeof(m->lane)); CG_LINE_NEXT_FIELD(b, len, p); rc = str2u32(b, p - b, &m->file_num_in_lane); CG_LINE_NEXT_FIELD(b, len, p); rc = str2u64(b, p - b, &m->dnb_offset_in_lane_file); CG_LINE_NEXT_FIELD(b, len, p); rc = str2u16(b, p - b, &m->allele_index); CG_LINE_NEXT_FIELD(b, len, p); rc = str2buf(b, p - b, tmp, sizeof(tmp)); if( tmp[0] != 'L' && tmp[0] != 'R' ) { rc = RC(rcRuntime, rcFile, rcReading, rcData, rcOutofrange); } m->side = tmp[0]; CG_LINE_NEXT_FIELD(b, len, p); rc = str2buf(b, p - b, tmp, sizeof(tmp)); if( tmp[0] != '+' && tmp[0] != '-' ) { rc = RC(rcRuntime, rcFile, rcReading, rcData, rcOutofrange); } m->strand = tmp[0]; CG_LINE_NEXT_FIELD(b, len, p); rc = str2i32(b, p - b, &m->offset_in_allele); CG_LINE_NEXT_FIELD(b, len, p); rc = str2buf(b, p - b, m->allele_alignment, sizeof(m->allele_alignment)); m->allele_alignment_length = p - b; CG_LINE_NEXT_FIELD(b, len, p); rc = str2i32(b, p - b, &m->offset_in_reference); CG_LINE_NEXT_FIELD(b, len, p); rc = str2buf(b, p - b, reference_alignment, sizeof(reference_alignment)); CG_LINE_NEXT_FIELD(b, len, p); rc = str2i32(b, p - b, &mate_offset_in_reference); CG_LINE_NEXT_FIELD(b, len, p); rc = str2buf(b, p - b, mate_reference_alignment, sizeof(mate_reference_alignment)); CG_LINE_NEXT_FIELD(b, len, p); rc = str2buf(b, p - b, tmp, sizeof(tmp)); if( tmp[0] < 33 || tmp[0] > 126 ) { rc = RC(rcRuntime, rcFile, rcReading, rcData, rcOutofrange); } m->mapping_quality = tmp[0]; for (i = 0; i < score_allele_num; ++i) { CG_LINE_NEXT_FIELD(b, len, p); rc = str2u16(b, p - b, &score_allele[i]); if(rc){ score_allele[i] =0; rc =0; } } CG_LINE_NEXT_FIELD(b, len, p); m->read_len = p - b; rc = str2buf(b, m->read_len, m->read, sizeof(m->read)); CG_LINE_LAST_FIELD(b, len, p); if( m->read_len != p - b ) { rc = RC(rcRuntime, rcFile, rcReading, rcData, rcInconsistent); } else { rc = str2buf(b, p - b, qual, sizeof(qual)); } ((CGEvidenceDnbs15*)cself)->records++; if( strcmp(next_interval_id, data->interval_id) != 0 ) { if (score_allele_num == 3) { DEBUG_MSG(10, ("%3u evidenceDnbs: '%s'\t'%s'\t'%s'\t'%s'\t%u\t%lu\t%hu\t%c\t%c\t%i\t'%.*s'" "\t%i\t'%s'\t%i\t'%s'\t%c\t%hu\t%hu\t%hu\t'%.*s'\t'%s'\n", data->qty, next_interval_id, m->chr, m->slide, m->lane, m->file_num_in_lane, m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele, m->allele_alignment_length, m->allele_alignment, m->offset_in_reference, reference_alignment, mate_offset_in_reference, mate_reference_alignment, m->mapping_quality, score_allele[0], score_allele[1], score_allele[2], m->read_len, m->read, qual)); } else if (score_allele_num == 4) { DEBUG_MSG(10, ("%3u evidenceDnbs: '%s'\t'%s'\t'%s'\t'%s'\t%u\t%lu\t%hu\t%c\t%c\t%i\t'%.*s'" "\t%i\t'%s'\t%i\t'%s'\t%c\t%hu\t%hu\t%hu\t%hu\t'%.*s'\t'%s'\n", data->qty, next_interval_id, m->chr, m->slide, m->lane, m->file_num_in_lane, m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele, m->allele_alignment_length, m->allele_alignment, m->offset_in_reference, reference_alignment, mate_offset_in_reference, mate_reference_alignment, m->mapping_quality, score_allele[0], score_allele[1], score_allele[2], score_allele[3], m->read_len, m->read, qual)); } else { assert(0); } } CG_LINE_END(); if( next_interval_id[0] == '\0' ) { break; } if( strcmp(next_interval_id, data->interval_id) != 0 ) { /* next record is from next interval, remeber it and stop */ memcpy(&next_rec, m, sizeof(next_rec)); data->qty--; break; } } while( rc == 0 ); return rc; }