Author: tille Date: 2015-07-05 18:03:41 +0000 (Sun, 05 Jul 2015) New Revision: 19527
Modified: trunk/packages/bowtie/trunk/debian/changelog trunk/packages/bowtie/trunk/debian/patches/bowtie_ContextLss-1.1-1.4.patch trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch Log: New upstream version, refreshed patches Modified: trunk/packages/bowtie/trunk/debian/changelog =================================================================== --- trunk/packages/bowtie/trunk/debian/changelog 2015-07-05 17:14:00 UTC (rev 19526) +++ trunk/packages/bowtie/trunk/debian/changelog 2015-07-05 18:03:41 UTC (rev 19527) @@ -1,3 +1,9 @@ +bowtie (1.1.2-1) UNRELEASED; urgency=medium + + * New upstream version + + -- Andreas Tille <[email protected]> Sun, 05 Jul 2015 20:02:01 +0200 + bowtie (1.1.1-2) unstable; urgency=high * Team upload. Modified: trunk/packages/bowtie/trunk/debian/patches/bowtie_ContextLss-1.1-1.4.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/bowtie_ContextLss-1.1-1.4.patch 2015-07-05 17:14:00 UTC (rev 19526) +++ trunk/packages/bowtie/trunk/debian/patches/bowtie_ContextLss-1.1-1.4.patch 2015-07-05 18:03:41 UTC (rev 19527) @@ -6,7 +6,7 @@ --- a/diff_sample.h +++ b/diff_sample.h -@@ -853,7 +856,7 @@ +@@ -856,7 +856,7 @@ void DifferenceCoverSample<TStr>::build( { Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose()); VMSG_NL(" Invoking Larsson-Sadakane on ranks"); @@ -15,4 +15,3 @@ c.suffixsort( (TIndexOff*)begin(_isaPrime, Standard()), (TIndexOff*)begin(sPrime, Standard()), - Modified: trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch 2015-07-05 17:14:00 UTC (rev 19526) +++ trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch 2015-07-05 18:03:41 UTC (rev 19527) @@ -7,7 +7,7 @@ --- a/Makefile +++ b/Makefile -@@ -126,8 +126,8 @@ ifeq (32,$(BITS)) +@@ -143,8 +143,8 @@ ifeq (32,$(BITS)) $(error bowtie2 compilation requires a 64-bit platform ) endif Modified: trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch 2015-07-05 17:14:00 UTC (rev 19526) +++ trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch 2015-07-05 18:03:41 UTC (rev 19527) @@ -7,7 +7,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ --- a/Makefile +++ b/Makefile -@@ -51,7 +51,9 @@ endif +@@ -58,7 +58,9 @@ endif LINUX = 0 ifneq (,$(findstring Linux,$(shell uname))) LINUX = 1 Modified: trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch 2015-07-05 17:14:00 UTC (rev 19526) +++ trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch 2015-07-05 18:03:41 UTC (rev 19527) @@ -214,7 +214,7 @@ const bool reportSe_; --- a/ebwt_search.cpp +++ b/ebwt_search.cpp -@@ -110,7 +110,7 @@ static bool strandFix; // attempt to fi +@@ -111,7 +111,7 @@ static bool strandFix; // attempt to fi static bool randomizeQuals; // randomize quality values static bool stats; // print performance stats static int chunkPoolMegabytes; // max MB to dedicate to best-first search frames per thread @@ -223,7 +223,7 @@ static bool chunkVerbose; // have chunk allocator output status messages? static bool recal; static int recalMaxCycle; -@@ -222,7 +222,7 @@ static void resetOptions() { +@@ -223,7 +223,7 @@ static void resetOptions() { randomizeQuals = false; // randomize quality values stats = false; // print performance stats chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread @@ -232,7 +232,7 @@ chunkVerbose = false; // have chunk allocator output status messages? recal = false; recalMaxCycle = 64; -@@ -1192,7 +1192,7 @@ static void exactSearchWorkerStateful(vo +@@ -1201,7 +1201,7 @@ static void exactSearchWorkerStateful(vo PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); @@ -241,7 +241,7 @@ UnpairedExactAlignerV1Factory alSEfact( ebwt, NULL, -@@ -1361,7 +1361,7 @@ static void mismatchSearchWorkerFullStat +@@ -1385,7 +1385,7 @@ static void mismatchSearchWorkerFullStat // Global initialization PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); @@ -250,7 +250,7 @@ Unpaired1mmAlignerV1Factory alSEfact( ebwtFw, -@@ -1658,7 +1658,7 @@ static void twoOrThreeMismatchSearchWork +@@ -1687,7 +1687,7 @@ static void twoOrThreeMismatchSearchWork PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); @@ -259,7 +259,7 @@ Unpaired23mmAlignerV1Factory alSEfact( ebwtFw, &ebwtBw, -@@ -2091,7 +2091,7 @@ static void seededQualSearchWorkerFullSt +@@ -2156,7 +2156,7 @@ static void seededQualSearchWorkerFullSt // Global initialization PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid); HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink); Modified: trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch 2015-07-05 17:14:00 UTC (rev 19526) +++ trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch 2015-07-05 18:03:41 UTC (rev 19527) @@ -6,7 +6,7 @@ --- a/Makefile +++ b/Makefile -@@ -198,7 +198,7 @@ DEFS=-fno-strict-aliasing \ +@@ -215,7 +215,7 @@ DEFS=-fno-strict-aliasing \ $(MM_DEF) \ $(SHMEM_DEF) Modified: trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch =================================================================== --- trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2015-07-05 17:14:00 UTC (rev 19526) +++ trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2015-07-05 18:03:41 UTC (rev 19527) @@ -6,16 +6,16 @@ --- a/Makefile +++ b/Makefile -@@ -2,7 +2,7 @@ - # Makefile for bowtie, bowtie-build, bowtie-inspect - # +@@ -5,7 +5,7 @@ + prefix = /usr/local + bindir = $(prefix)/bin -SEQAN_DIR = SeqAn-1.1 +SEQAN_DIR = /usr/include/seqan SEQAN_INC = -I $(SEQAN_DIR) INC = $(SEQAN_INC) -I third_party CPP = g++ -@@ -151,7 +151,6 @@ GENERAL_LIST = $(wildcard scripts/*.sh) +@@ -168,7 +168,6 @@ GENERAL_LIST = $(wildcard scripts/*.sh) $(wildcard genomes/NC_008253.fna) \ $(wildcard reads/e_coli_1000.*) \ $(wildcard reads/e_coli_1000_*) \ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
