Commit 142f48e4 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 1.0.3

parent a066562d

src/holders.hpp

+10 −1
Original line number Diff line number Diff line
@@ -385,7 +385,16 @@ public: 
                            ArrayGaps>;

    using TAlignRow1 = Gaps<typename Infix<typename Value<typename TGlobalHolder::TTransSubjSeqs>::Type>::Type,

                            ArrayGaps>;

#if (SEQAN_VERSION_MINOR < 4)

    using TDPContext =  DPContext<typename Value<typename TGlobalHolder::TScoreScheme>::Type, TScoreExtension>;

#else

    using TCellValue  = int16_t;

    using TDPCell     = DPCell_<TCellValue, TScoreExtension>;

    using TTraceValue = typename TraceBitMap_<TCellValue>::Type;

    using TScoreHost  = String<TDPCell, Alloc<OverAligned> >;

    using TTraceHost  = String<TTraceValue, Alloc<OverAligned> >;

    using TDPContext  = DPContext<TDPCell, TTraceValue, TScoreHost, TTraceHost>;

#endif

    using TAliExtContext = AliExtContext_<TAlignRow0, TAlignRow1, TDPContext>;



    TAliExtContext      alignContext;

src/options.hpp

+3 −3
Original line number Diff line number Diff line
@@ -420,14 +420,14 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv) 
        "Query sequences.",

        ArgParseArgument::INPUT_FILE,

        "IN"));

    setValidValues(parser, "query", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));

    setValidValues(parser, "query", getFileExtensions(SeqFileIn()));

    setRequired(parser, "q");



    addOption(parser, ArgParseOption("d", "database",

        "Path to original database sequences (a precomputed index with .sa or .fm needs to exist!).",

        ArgParseArgument::INPUT_FILE,

        "IN"));

    setValidValues(parser, "database", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));

    setValidValues(parser, "database", getFileExtensions(SeqFileIn()));

    setRequired(parser, "d");



    addOption(parser, ArgParseOption("di", "db-index-type",
@@ -1048,7 +1048,7 @@ parseCommandLine(LambdaIndexerOptions & options, int argc, char const ** argv) 
        ArgParseArgument::INPUT_FILE,

        "IN"));

    setRequired(parser, "database");

    setValidValues(parser, "database", toCString(concat(getFileExtensions(SeqFileIn()), ' ')));

    setValidValues(parser, "database", getFileExtensions(SeqFileIn()));



    addOption(parser, ArgParseOption("s",

        "segfile",