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corrected database vector for proteinaln2nucl

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AnnSeidel committed Jul 11, 2019
1 parent 0383bcc commit 7e90de41405ba069fb7012a20fe2e53a11143730
Showing with 6 additions and 4 deletions.
  1. +5 −3 src/mmseqs.cpp
  2. +1 −1 src/util/proteinaln2nucl.cpp
@@ -621,9 +621,11 @@ std::vector<struct Command> commands = {
"Map protein alignment to nucleotide alignment",
NULL,
"Martin Steinegger <martin.steinegger@mpibpc.mpg.de> ",
"<i:queryDB> <i:targetDB> <i:alnDB> <o:alnDB>",
CITATION_MMSEQS2, {{"queryDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb },
{"targetDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb },
"<i:nuclQueryDB> <i:nuclTargetDB> <i:aaQueryDB> <i:aaTargetDB> <i:alnDB> <o:alnDB>",
CITATION_MMSEQS2, {{"nuclQueryDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb },
{"nuclTargetDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb },
{"aaQueryDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb },
{"aaTargetDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb },
{"alnDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::alignmentDb },
{"alnDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::alignmentDb }}},
{"tsv2db", tsv2db, &par.tsv2db, COMMAND_DB,
@@ -13,7 +13,7 @@

int proteinaln2nucl(int argc, const char **argv, const Command &command) {
Parameters &par = Parameters::getInstance();
par.parseParameters(argc, argv, command, false, 0, 0);
par.parseParameters(argc, argv, command, true, 0, 0);

DBReader<unsigned int> *qdbr_nuc = new DBReader<unsigned int>(par.db1.c_str(), par.db1Index.c_str(), par.threads, DBReader<unsigned int>::USE_INDEX|DBReader<unsigned int>::USE_DATA);
qdbr_nuc->open(DBReader<unsigned int>::NOSORT);

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