1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
#include <pbdata/sam/ReferenceSequence.hpp>
const char* SAMReferenceSequence::SAMReferenceSequenceFieldNames[] = {"SN", "LN"};
void SAMReferenceSequence::StoreValues(std::vector<SAMKeywordValuePair>& kvPairs,
uint64_t lineNumber)
{
(void)(lineNumber);
std::vector<bool> usedFields;
usedFields.resize(SQ_LN);
std::fill(usedFields.begin(), usedFields.end(), false);
for (size_t i = 0; i < kvPairs.size(); i++) {
if (kvPairs[i].key == "SN") {
sequenceName = kvPairs[i].value;
usedFields[SQ_SN] = true;
} else if (kvPairs[i].key == "LN") {
StoreValue(kvPairs[i].value, length);
usedFields[SQ_SN] = true;
}
}
for (size_t i = 0; i < usedFields.size(); i++) {
if (usedFields[i] == false) {
std::cout << "SQ specifier missing " << SAMReferenceSequenceFieldNames[i] << std::endl;
}
}
}
const char* SAMFullReferenceSequence::SAMFullReferenceSequenceFieldNames[] = {"AS", "M5", "SP",
"UR"};
void SAMFullReferenceSequence::StoreValues(std::vector<SAMKeywordValuePair>& kvPairs,
uint64_t lineNumber)
{
SAMReferenceSequence::StoreValues(kvPairs, lineNumber);
for (size_t i = 0; i < kvPairs.size(); i++) {
if (kvPairs[i].key == "AS") {
genomeAssembly = kvPairs[i].value;
} else if (kvPairs[i].key == "M5") {
md5 = kvPairs[i].value;
} else if (kvPairs[i].key == "SP") {
species = kvPairs[i].value;
} else if (kvPairs[i].key == "UR") {
uri = kvPairs[i].value;
}
}
}
|
