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Add createdb support for sequence db input #545

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Add createdb support for sequence db input #545

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ebaedb7
Fix createdb support for db input
matchy233 Mar 2, 2022
ece8e5d
Match coding convention
matchy233 Mar 16, 2022
e34f40d
Update usage text with introduction for db input
matchy233 Mar 16, 2022
cdb5c8a
Add back support for generic db
matchy233 Mar 16, 2022
f9eb35d
Update usage text for createdb with more details
matchy233 Mar 16, 2022
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10 changes: 9 additions & 1 deletion src/util/createdb.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -98,9 +98,12 @@ int createdb(int argc, const char **argv, const Command& command) {

size_t fileCount = filenames.size();
DBReader<unsigned int>* reader = NULL;
DBReader<unsigned int>* hdrReader = nullptr;
if (dbInput == true) {
reader = new DBReader<unsigned int>(par.db1.c_str(), par.db1Index.c_str(), 1, DBReader<unsigned int>::USE_DATA | DBReader<unsigned int>::USE_INDEX | DBReader<unsigned int>::USE_LOOKUP);
reader->open(DBReader<unsigned int>::LINEAR_ACCCESS);
hdrReader = new DBReader<unsigned int>((par.db1 + "_h").c_str(), (par.db1 + "_h.index").c_str(), 1, DBReader<unsigned int>::USE_DATA | DBReader<unsigned int>::USE_INDEX);
hdrReader->open(DBReader<unsigned int>::LINEAR_ACCCESS);
fileCount = reader->getSize();
}

Expand All @@ -126,8 +129,11 @@ int createdb(int argc, const char **argv, const Command& command) {
}

KSeqWrapper* kseq = NULL;
std::string seq = ">";
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@martin-steinegger martin-steinegger Mar 16, 2022

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Can we move this into the if condition?

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@matchy233 matchy233 Mar 16, 2022

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No we can't :( we need to refer to the address of this string later. Variables defined inside if {} block is not accessible to the outer scope.

if (dbInput == true) {
kseq = new KSeqBuffer(reader->getData(fileIdx, 0), reader->getEntryLen(fileIdx) - 1);
seq.append(hdrReader->getData(fileIdx, 0));
seq.append(reader->getData(fileIdx, 0));
kseq = new KSeqBuffer(seq.c_str(), seq.length());
} else {
kseq = KSeqFactory(filenames[fileIdx].c_str());
}
Expand Down Expand Up @@ -260,6 +266,8 @@ int createdb(int argc, const char **argv, const Command& command) {
if (dbInput == true) {
reader->close();
delete reader;
hdrReader->close();
delete hdrReader;
}

if (entries_num == 0) {
Expand Down