[med-svn] r19527 - in trunk/packages/bowtie/trunk/debian: . patches

Andreas Tille tille at moszumanska.debian.org
Sun Jul 5 18:03:42 UTC 2015 

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 <tille at debian.org>  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_*) \

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