Michael R. Crusoe pushed to branch upstream at Debian Med / lambda-align
Commits: 142f48e4 by Michael R. Crusoe at 2018-02-17T09:30:44-08:00 New upstream version 1.0.3 - - - - - 2 changed files: - src/holders.hpp - src/options.hpp Changes: ===================================== src/holders.hpp ===================================== --- a/src/holders.hpp +++ b/src/holders.hpp @@ -385,7 +385,16 @@ public: ArrayGaps>; using TAlignRow1 = Gaps<typename Infix<typename Value<typename TGlobalHolder::TTransSubjSeqs>::Type>::Type, ArrayGaps>; - using TDPContext = DPContext<typename Value<typename TGlobalHolder::TScoreScheme>::Type, TScoreExtension>; +#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 ===================================== --- a/src/options.hpp +++ b/src/options.hpp @@ -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", View it on GitLab: https://salsa.debian.org/med-team/lambda-align/commit/142f48e49a0036a7836f9afdd24d666432a6c95e --- View it on GitLab: https://salsa.debian.org/med-team/lambda-align/commit/142f48e49a0036a7836f9afdd24d666432a6c95e You're receiving this email because of your account on salsa.debian.org.
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