This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository lambda-align.
commit 78d8176660deef5e2b6c0f7e629fa51392cd063e Author: Andreas Tille <[email protected]> Date: Sun Dec 18 09:21:05 2016 +0100 Refresh patches --- debian/patches/cast-min-initializer.patch | 2 +- debian/patches/fix-documentation.patch | 30 +++++++++++++++--------------- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/debian/patches/cast-min-initializer.patch b/debian/patches/cast-min-initializer.patch index e61163a..7e0ec0b 100644 --- a/debian/patches/cast-min-initializer.patch +++ b/debian/patches/cast-min-initializer.patch @@ -7,7 +7,7 @@ Forwarded: https://github.com/seqan/lambda/issues/68 Applied-Upstream: https://github.com/seqan/lambda/commit/cdb7e755af9829e26bf6e5f9ddbb07b5102038ef --- a/src/lambda.hpp +++ b/src/lambda.hpp -@@ -701,8 +701,8 @@ +@@ -784,8 +784,8 @@ seedLooksPromising(LocalDataHolder<TGlob } effectiveLength = std::min({ diff --git a/debian/patches/fix-documentation.patch b/debian/patches/fix-documentation.patch index 3fa5502..a62d8e7 100644 --- a/debian/patches/fix-documentation.patch +++ b/debian/patches/fix-documentation.patch @@ -2,20 +2,9 @@ Description: fix documentation strings Author: Sascha Steinbiss <[email protected]> Forwarded: https://github.com/seqan/lambda/pull/65 Applied-Upstream: https://github.com/seqan/lambda/pull/65 ---- a/src/holders.hpp -+++ b/src/holders.hpp -@@ -174,7 +174,7 @@ - << "\033[0m\n\n"; - - if (rem != stats.hitsFinal) -- std::cout << "WARNING: hits dont add up\n"; -+ std::cout << "WARNING: hits don't add up\n"; - } - - if (options.verbosity >= 1) --- a/src/options.hpp +++ b/src/options.hpp -@@ -587,14 +587,14 @@ +@@ -615,14 +615,14 @@ parseCommandLine(LambdaOptions & options // "STR")); // setValidValues(parser, "query-alphabet", "dna5 aminoacid"); // setDefaultValue(parser, "query-alphabet", "dna5"); @@ -32,7 +21,7 @@ Applied-Upstream: https://github.com/seqan/lambda/pull/65 // addOption(parser, ArgParseOption("sa", "seeding-alphabet", // "alphabet to use during seeding (reduction possible)", // ArgParseArgument::STRING, -@@ -710,7 +710,7 @@ +@@ -754,7 +754,7 @@ parseCommandLine(LambdaOptions & options addSection(parser, "Scoring"); addOption(parser, ArgParseOption("sc", "scoring-scheme", @@ -41,14 +30,14 @@ Applied-Upstream: https://github.com/seqan/lambda/pull/65 "[ignored for BlastN]", ArgParseArgument::INTEGER)); setDefaultValue(parser, "scoring-scheme", "62"); -@@ -1033,12 +1033,14 @@ +@@ -1128,12 +1128,14 @@ parseCommandLine(LambdaIndexerOptions & // Setup ArgumentParser. ArgumentParser parser("lambda_indexer"); + setShortDescription(parser, "indexer for creating lambda-compatible databases"); + // Define usage line and long description. - addUsageLine(parser, "[\\fIOPTIONS\\fP] \\-d DATABASE.fasta\\fP"); + addUsageLine(parser, "[\\fIOPTIONS\\fP] \\-d DATABASE.fasta [-i INDEX.lambda]\\fP"); sharedSetup(parser); @@ -57,3 +46,14 @@ Applied-Upstream: https://github.com/seqan/lambda/pull/65 addSection(parser, "Input Options"); addOption(parser, ArgParseOption("d", "database", +--- a/src/holders.hpp ++++ b/src/holders.hpp +@@ -199,7 +199,7 @@ void printStats(StatsHolder const & stat + << "\033[0m\n\n"; + + if (rem != stats.hitsFinal) +- std::cout << "WARNING: hits dont add up\n"; ++ std::cout << "WARNING: hits don't add up\n"; + + std::cout << "Detailed Non-Wall-Clock times:\n" + << " genSeeds: " << stats.timeGenSeeds << "\n" -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/lambda-align.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
