fixed problems in hybridassembler approach with new mmseqs parameter …

…validation
soedinglab · Jul 11, 2019 · da18dca · da18dca
1 parent e9bf462
commit da18dca
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Showing 4 changed files with 9 additions and 7 deletions.
diff --git a/data/hybridassembler.sh b/data/hybridassembler.sh
@@ -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

diff --git a/lib/mmseqs b/lib/mmseqs
diff --git a/src/assembler/mergereads.cpp b/src/assembler/mergereads.cpp
@@ -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";
 

diff --git a/src/plass.cpp b/src/plass.cpp
@@ -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,