void init_library_table()
{
ReadGroupProperties fr_unstranded;
fr_unstranded.platform(UNKNOWN_PLATFORM);
fr_unstranded.mate_strand_mapping(FR);
fr_unstranded.std_mate_orientation(MATES_POINT_TOWARD);
fr_unstranded.strandedness(UNSTRANDED_PROTOCOL);
library_type_table["fr-unstranded"] = fr_unstranded;
ReadGroupProperties fr_firststrand;
fr_firststrand.platform(UNKNOWN_PLATFORM);
fr_firststrand.mate_strand_mapping(RF);
fr_firststrand.std_mate_orientation(MATES_POINT_TOWARD);
fr_firststrand.strandedness(STRANDED_PROTOCOL);
library_type_table["fr-firststrand"] = fr_firststrand;
ReadGroupProperties fr_secondstrand;
fr_secondstrand.platform(UNKNOWN_PLATFORM);
fr_secondstrand.mate_strand_mapping(FR);
fr_secondstrand.std_mate_orientation(MATES_POINT_TOWARD);
fr_secondstrand.strandedness(STRANDED_PROTOCOL);
library_type_table["fr-secondstrand"] = fr_secondstrand;
ReadGroupProperties ff_unstranded;
ff_unstranded.platform(UNKNOWN_PLATFORM);
ff_unstranded.mate_strand_mapping(FF);
ff_unstranded.std_mate_orientation(MATES_POINT_TOWARD);
ff_unstranded.strandedness(UNSTRANDED_PROTOCOL);
library_type_table["ff-unstranded"] = ff_unstranded;
ReadGroupProperties ff_firststrand;
ff_firststrand.platform(UNKNOWN_PLATFORM);
ff_firststrand.mate_strand_mapping(FF);
ff_firststrand.std_mate_orientation(MATES_POINT_TOWARD);
ff_firststrand.strandedness(STRANDED_PROTOCOL);
library_type_table["ff-firststrand"] = ff_firststrand;
ReadGroupProperties ff_secondstrand;
ff_secondstrand.platform(UNKNOWN_PLATFORM);
ff_secondstrand.mate_strand_mapping(RR);
ff_secondstrand.std_mate_orientation(MATES_POINT_TOWARD);
ff_secondstrand.strandedness(STRANDED_PROTOCOL);
library_type_table["ff-secondstrand"] = ff_secondstrand;
ReadGroupProperties transfrags;
transfrags.platform(UNKNOWN_PLATFORM);
transfrags.mate_strand_mapping(FR);
transfrags.std_mate_orientation(MATES_POINT_TOWARD);
transfrags.strandedness(UNSTRANDED_PROTOCOL);
transfrags.complete_fragments(true);
library_type_table["transfrags"] = transfrags;
//global_read_properties = &(library_type_table.find(default_library_type)->second);
}
// Parses the header to determine platform and other properties
bool HitFactory::parse_header_string(const string& header_rec,
ReadGroupProperties& rg_props)
{
vector<string> columns;
tokenize(header_rec, "\t", columns);
if (columns[0] == "@RG")
{
for (size_t i = 1; i < columns.size(); ++i)
{
vector<string> fields;
tokenize(columns[i], ":", fields);
if (fields[0] == "PL")
{
if (rg_props.platform() == UNKNOWN_PLATFORM)
{
Platform p = str_to_platform(fields[1]);
rg_props.platform(p);
}
else
{
Platform p = str_to_platform(fields[1]);
if (p != rg_props.platform())
{
fprintf(stderr, "Error: Processing reads from different platforms is not currently supported\n");
return false;
}
}
}
}
}
else if (columns[0] == "@SQ")
{
_num_seq_header_recs++;
for (size_t i = 1; i < columns.size(); ++i)
{
vector<string> fields;
tokenize(columns[i], ":", fields);
if (fields[0] == "SN")
{
// Populate the RefSequenceTable with the sequence dictionary,
// to ensure that (for example) downstream GTF files are sorted
// in an order consistent with the header, and to enforce that
// BAM records appear in the order implied by the header
RefID _id = _ref_table.get_id(fields[1], NULL);
const RefSequenceTable::SequenceInfo* info = _ref_table.get_info(_id);
if (info->observation_order != _num_seq_header_recs)
{
if (info->name != fields[1])
{
fprintf(stderr, "Error: Hash collision between references '%s' and '%s'.\n", info->name, fields[1].c_str());
}
else
{
fprintf(stderr, "Error: sort order of reads in BAMs must be the same\n");
}
exit(1);
}
}
}
}
return true;
}
