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fixed problems in hybridassembler approach with new mmseqs parameter …

…validation
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AnnSeidel committed Jul 11, 2019
1 parent e9bf462 commit da18dca3b2f368bdd94593b47f4bf8bf023238b0
Showing with 9 additions and 7 deletions.
  1. +1 −1 data/hybridassembler.sh
  2. +1 −1 lib/mmseqs
  3. +2 −2 src/assembler/mergereads.cpp
  4. +5 −3 src/plass.cpp
@@ -89,7 +89,7 @@ while [ $STEP -lt $NUM_IT ]; do
# 3. Ungapped alignment protein 2 nucl
if notExists "${TMP_PATH}/aln_nucl_$STEP"; then
"$MMSEQS" proteinaln2nucl "$INPUT_NUCL" "$INPUT_NUCL" "$INPUT_AA" "$INPUT_AA" "${TMP_PATH}/aln_$STEP" "${TMP_PATH}/aln_nucl_$STEP" \
|| fail "Ungapped alignment step died"
|| fail "Ungapped alignment 2 nucl step died"
fi

# 4. Assemble
@@ -99,8 +99,8 @@ int mergereads(int argn, const char **argv, const Command& command) {
free(r2);
free(r1);
}
resultWriter.close();
headerResultWriter.close();
resultWriter.close(true);
headerResultWriter.close(true);

Debug(Debug::INFO) << "\nDone.\n";

@@ -88,9 +88,11 @@ 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 }}},
{"kmermatcher", kmermatcher, &par.kmermatcher, COMMAND_EXPERT,

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