<pre style='margin:0'>
Renee Otten (reneeotten) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/30032d091fbf93d8da5cf5a1f1ec758ce3023a8a">https://github.com/macports/macports-ports/commit/30032d091fbf93d8da5cf5a1f1ec758ce3023a8a</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit 30032d091fbf93d8da5cf5a1f1ec758ce3023a8a
</span>Author: Kirill A. Korinsky <kirill@korins.ky>
AuthorDate: Mon Dec 5 23:15:25 2022 +0100
<span style='display:block; white-space:pre;color:#404040;'> bowtie: update to 1.3.1
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> Closes: https://trac.macports.org/ticket/65312
</span>---
science/bowtie/Portfile | 28 +-
science/bowtie/files/patch-Makefile.diff | 47 +--
science/bowtie/files/patch-seqan.diff | 559 -------------------------------
3 files changed, 33 insertions(+), 601 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bowtie/Portfile b/science/bowtie/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index caff697cecf..019fa42aac0 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bowtie/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bowtie/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,7 +3,7 @@
</span> PortSystem 1.0
PortGroup github 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup BenLangmead bowtie 1.2.3 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup BenLangmead bowtie 1.3.1 v
</span> revision 0
categories science biology
platforms darwin
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -21,12 +21,11 @@ long_description Bowtie is ${description}. It aligns short DNA sequences
</span>
homepage http://bowtie-bio.sourceforge.net/
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 a09f5d4dd685619ab60eef70b08c3b9d376bf85a \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 9a62e7959a11aa2229722e20800441ce4ecbb2f9e74dd29bd5b2c6f6e4553db8 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 7894211
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 c4aeaa1135bd40bbcbc38235878644d3b2b219da \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 1e087c6bef7415419902d06b5a4f9d5180fd1daf39b3752044e6b448e46e6a1b \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 7673131
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles-append patch-Makefile.diff \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patch-seqan.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles-append patch-Makefile.diff
</span>
post-patch {
reinplace -W ${worksrcpath} \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -36,13 +35,25 @@ post-patch {
</span> bowtie-inspect
}
<span style='display:block; white-space:pre;background:#e0ffe0;'>+# fix build on case insensitive FS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# In file included from bowtie_inspect.cpp:1:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/c++/v1/string:519:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/c++/v1/__debug:21:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/c++/v1/cstddef:37:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# ./version:1:1: error: expected unqualified-id
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# 1.3.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+post-extract {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ file delete ${worksrcpath}/VERSION
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+compiler.cxx_standard 2011
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> supported_archs x86_64 ppc64
installs_libs no
depends_build-append port:seqan-1
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_lib-append port:zlib \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- port:tbb
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append port:zlib
</span>
depends_run-append port:python27
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -66,7 +77,6 @@ post-destroot {
</span> MANUAL \
NEWS \
TUTORIAL \
<span style='display:block; white-space:pre;background:#ffe0e0;'>- VERSION \
</span> MANUAL.markdown \
${destroot}${prefix}/share/doc/${name}
}
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bowtie/files/patch-Makefile.diff b/science/bowtie/files/patch-Makefile.diff
</span><span style='display:block; white-space:pre;color:#808080;'>index e30eab17466..0fbed741365 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bowtie/files/patch-Makefile.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bowtie/files/patch-Makefile.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,29 +1,18 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- Makefile.orig 2017-12-12 11:29:54.000000000 -0700
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ Makefile 2019-01-27 04:52:46.000000000 -0700
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2,16 +2,18 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+diff --git Makefile Makefile
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+index fb98532..1afa4a1 100644
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- Makefile
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ Makefile
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2,7 +2,8 @@
</span> # Makefile for bowtie, bowtie-build, bowtie-inspect
#
-prefix = /usr/local
+include Makefile.macports.inc
<span style='display:block; white-space:pre;background:#ffe0e0;'>-+
</span> +prefix ?= /usr/local
bindir = $(prefix)/bin
<span style='display:block; white-space:pre;background:#ffe0e0;'>- SEQAN_DIR = ./SeqAn-1.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # treat SeqAn as a sysdir to suppress warnings
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- SEQAN_INC = -isystem $(SEQAN_DIR)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--CPP = g++
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--CXX = $(CPP)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--CC = gcc
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+CXX ?= g++
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+CPP ?= $(CXX)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+CC ?= gcc
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- HEADERS = $(wildcard *.h)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BOWTIE_MM = 1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -19,8 +21,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ARCH = $(shell uname -m)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -14,8 +15,8 @@ BOWTIE_SHARED_MEM = 1
</span> EXTRA_FLAGS =
EXTRA_CFLAGS =
EXTRA_CXXFLAGS =
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -31,16 +20,14 @@
</span> -CXXFLAGS += $(EXTRA_CXXFLAGS)
+CFLAGS += $(EXTRA_CFLAGS) $(CPPFLAGS)
+CXXFLAGS += $(EXTRA_CXXFLAGS) $(CPPFLAGS)
<span style='display:block; white-space:pre;background:#ffe0e0;'>- WARNING_FLAGS = -Wall -Wno-unused-parameter -Wno-reorder \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- -Wno-unused-local-typedefs
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ WARNING_FLAGS = -Wall -Wno-unused-parameter -Wno-reorder
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -49,14 +51,6 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RELEASE_DEPENDENCIES = $(if $(RELEASE_BUILD),static-libs)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -43,12 +44,6 @@ endif
</span> MACOS =
ifneq (,$(findstring Darwin,$(shell uname)))
MACOS = 1
- ifneq (,$(findstring 13,$(shell uname -r)))
<span style='display:block; white-space:pre;background:#ffe0e0;'>-- CPP = clang++
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- CC = clang
</span> - override EXTRA_FLAGS += -stdlib=libstdc++
- endif
- ifeq (1, $(RELEASE_BUILD))
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -49,12 +36,12 @@
</span> endif
LINUX =
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -159,29 +153,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -130,23 +125,8 @@ BUILD_CPPS_MAIN = $(BUILD_CPPS) bowtie_build_main.cpp
</span> SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
VERSION = $(shell cat VERSION)
-BITS=32
<span style='display:block; white-space:pre;background:#ffe0e0;'>--ifeq (x86_64,$(shell uname -m))
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-ifeq (1,$(shell echo __LP64__ | $(CC) -P -E - | tr -d '\n'))
</span> - BITS=64
-endif
-# msys will always be 32 bit so look at the cpu arch instead.
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -64,18 +51,12 @@
</span> - endif
-endif
-
<span style='display:block; white-space:pre;background:#ffe0e0;'>--ifeq (1,$(LINUX))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ifeq (x86_64, $(shell uname -p))
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- BITS=64
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- endif
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--endif
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--
</span> -ifeq (32,$(BITS))
- $(error bowtie2 compilation requires a 64-bit platform )
-endif
-
<span style='display:block; white-space:pre;background:#ffe0e0;'>--DEBUG_FLAGS = -O0 -g3 -m64
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--RELEASE_FLAGS = -O3 -m64
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-DEBUG_FLAGS = -O0 -g3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-RELEASE_FLAGS = -O3
</span> +DEBUG_FLAGS =
+RELEASE_FLAGS =
NOASSERT_FLAGS = -DNDEBUG
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bowtie/files/patch-seqan.diff b/science/bowtie/files/patch-seqan.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 9ed4f75adfb..00000000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bowtie/files/patch-seqan.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,559 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Description: Change class name of _Context_LSS
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- New version 1.4 of SeQan uses a different name of the class.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Forwarded: no
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Author: Gert Wollny <gw.fossdev@gmail.com>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Last-Update: 2014-100-06
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- diff_sample.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ diff_sample.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -979,7 +979,7 @@ void DifferenceCoverSample<TStr>::build(
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- VMSG_NL(" Invoking Larsson-Sadakane on ranks");
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- _Context_LSS<TIndexOff> c;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ ContextLss_<TIndexOff> c;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- c.suffixsort(
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- (TIndexOff*)begin(_isaPrime, Standard()),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- (TIndexOff*)begin(sPrime, Standard()),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Description: Proper type-casting in using seqan::_setBegin().
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- Required by newer versions of GCC.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Forwarded: no
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Author: Ognyan Kulev <ogi@debian.org>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Last-Update: 2013-04-18
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- pat.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ pat.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -120,13 +120,13 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ~Read() {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- clearAll(); reset();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Prevent seqan from trying to free buffers
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- _setBegin(patFw, NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- _setBegin(patRc, NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- _setBegin(qual, NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- _setBegin(patFwRev, NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- _setBegin(patRcRev, NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- _setBegin(qualRev, NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- _setBegin(name, NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ _setBegin(patFw, (Dna5*)NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ _setBegin(patRc, (Dna5*)NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ _setBegin(qual, (char*)NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ _setBegin(patFwRev, (Dna5*)NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ _setBegin(patRcRev, (Dna5*)NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ _setBegin(qualRev, (char*)NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ _setBegin(name, (char*)NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- #define RESET_BUF(str, buf, typ) _setBegin(str, (typ*)buf); _setLength(str, 0); _setCapacity(str, BUF_SIZE);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Description: Use SeqAn 1.4's seqan::popCount() function instead of own function
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Author: Ognyan Kulev <ogi@debian.org>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Last-Update: 2014-03-08
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>----
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- diff_sample.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ diff_sample.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -481,6 +481,8 @@ static String<T> getDeltaMap(T v, const
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- return amap;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+// Debian: Use seqan::popCount
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#if 0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- /**
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- * Return population count (count of all bits set to 1) of i.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -493,6 +495,7 @@ static unsigned int popCount(T i) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- return cnt;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+#endif
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- /**
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- * Calculate log-base-2 of i
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Description: Renamed ChunkPool class to bowtieChunkPool.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- SeqAn has a class with the same name and fatal name collision happens.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Forwarded: no
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Author: Ognyan Kulev <ogi@debian.org>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Last-Update: 2013-04-18
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- aligner.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ aligner.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -391,7 +391,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool verbose,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool quiet,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int maxBts,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int *btCnt = NULL,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- AlignerMetrics *metrics = NULL) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- Aligner(true, rangeMode),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -597,7 +597,7 @@ protected:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool quiet_; // don't print informational/warning info
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const int maxBts_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int *btCnt_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- AlignerMetrics *metrics_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- };
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -638,7 +638,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool verbose,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool quiet,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int maxBts,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int *btCnt) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- Aligner(true, rangeMode),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- refs_(refs),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1405,7 +1405,7 @@ protected:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool quiet_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int maxBts_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int *btCnt_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Range-finding state for first mate
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1529,7 +1529,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool verbose,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool quiet,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int maxBts,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int *btCnt) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- Aligner(true, rangeMode),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- refs_(refs),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2076,7 +2076,7 @@ protected:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- TDriver* driver_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Pool for distributing chunks of best-first path descriptor memory
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool verbose_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool quiet_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- aligner_0mm.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ aligner_0mm.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -32,7 +32,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache* cacheFw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache* cacheBw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool maqPenalty,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -123,7 +123,7 @@ private:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool maqPenalty_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -162,7 +162,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache* cacheFw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache* cacheBw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool reportSe,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -363,7 +363,7 @@ private:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const bool reportSe_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- aligner_1mm.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ aligner_1mm.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -32,7 +32,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool maqPenalty,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -160,7 +160,7 @@ private:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const bool maqPenalty_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -199,7 +199,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool reportSe,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -475,7 +475,7 @@ private:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const bool reportSe_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- aligner_23mm.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ aligner_23mm.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -33,7 +33,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool maqPenalty,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -230,7 +230,7 @@ private:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const bool maqPenalty_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -271,7 +271,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool reportSe,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -672,7 +672,7 @@ private:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const bool reportSe_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- aligner_seed_mm.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ aligner_seed_mm.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -37,7 +37,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache* cacheFw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache* cacheBw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool maqPenalty,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -554,7 +554,7 @@ private:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool strandFix_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -598,7 +598,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache* cacheFw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache* cacheBw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool reportSe,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1375,7 +1375,7 @@ private:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const bool reportSe_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- ebwt_search.cpp
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ ebwt_search.cpp
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -125,7 +125,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- static bool strandFix; // attempt to fix strand bias
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- static bool stats; // print performance stats
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- static int chunkPoolMegabytes; // max MB to dedicate to best-first search frames per thread
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--static int chunkSz; // size of single chunk disbursed by ChunkPool
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+static int chunkSz; // size of single chunk disbursed by bowtieChunkPool
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- static bool chunkVerbose; // have chunk allocator output status messages?
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- static bool useV1;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- static bool reportSe;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -232,7 +232,7 @@ norc = false; // don't align rc orientation of read
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- strandFix = true; // attempt to fix strand bias
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- stats = false; // print performance stats
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- chunkSz = 256; // size of single chunk disbursed by ChunkPool (in KB)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ chunkSz = 256; // size of single chunk disbursed by bowtieChunkPool (in KB)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- chunkVerbose = false; // have chunk allocator output status messages?
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- useV1 = true;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- reportSe = false;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1343,7 +1343,7 @@ static void exactSearchWorkerStateful(vo
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- UnpairedExactAlignerV1Factory alSEfact(
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ebwt,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- NULL,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1632,7 +1632,7 @@ static void mismatchSearchWorkerFullStat
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Global initialization
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- Unpaired1mmAlignerV1Factory alSEfact(
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ebwtFw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2083,7 +2083,7 @@ static void twoOrThreeMismatchSearchWork
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- Unpaired23mmAlignerV1Factory alSEfact(
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ebwtFw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- &ebwtBw,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2753,7 +2753,7 @@ static void seededQualSearchWorkerFullSt
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Global initialization
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- AlignerMetrics *metrics = NULL;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if(stats) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- ebwt_search_backtrack.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ ebwt_search_backtrack.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2703,7 +2703,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool verbose,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool quiet,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool mate1,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int *btCnt) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- SingleRangeSourceDriver<EbwtRangeSource>(
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- params, rs, fw, sink, sinkPt, os, verbose,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2877,7 +2877,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool verbose,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool quiet,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool mate1,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int *btCnt = NULL) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- params_(params),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- rs_(rs),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2936,7 +2936,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool verbose_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool quiet_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool mate1_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool* pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool* pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int *btCnt_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- };
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- pool.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ pool.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -19,13 +19,13 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- * is set at construction time. Heap memory is only allocated at
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- * construction and deallocated at destruction.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--class ChunkPool {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+class bowtieChunkPool {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- /**
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- * Initialize a new pool with an initial size of about 'bytes'
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- * bytes. Exit with an error message if we can't allocate it.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- verbose(verbose_), patid(0), pool_(NULL), cur_(0),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bits_(lim_), exhaustCrash_(false),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -38,7 +38,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- } catch(std::bad_alloc& e) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ThreadSafe _ts(&gLock);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- std::cerr << "Error: Could not allocate ChunkPool of "
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ std::cerr << "Error: Could not allocate bowtieChunkPool of "
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- << totSz << " bytes" << std::endl;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- exhausted();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- throw 1; // Exit if we haven't already
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -48,7 +48,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- /**
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- * Delete all the pools.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ~ChunkPool() {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ ~bowtieChunkPool() {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if(pool_ != NULL) delete[] pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -189,7 +189,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- * Initialize a new pool with an initial size of about 'bytes'
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- * bytes. Exit with an error message if we can't allocate it.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- */
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- AllocOnlyPool(ChunkPool* pool, const char *name) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ AllocOnlyPool(bowtieChunkPool* pool, const char *name) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- pool_(pool), name_(name), curPool_(0), cur_(0)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- assert(pool != NULL);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -388,7 +388,7 @@ protected:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- lastCurInPool_.pop_back();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool* pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool* pool_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const char *name_;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- std::vector<T*> pools_; /// the memory pools
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t curPool_; /// pool we're current allocating from
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- range_source.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ range_source.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1307,7 +1307,7 @@ class PathManager {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- PathManager(ChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ PathManager(bowtieChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- branchQ_(verbose, quiet),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- cpool(cpool_),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bpool(cpool, "branch"),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1556,7 +1556,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool *cpool; // pool for generic chunks of memory
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool *cpool; // pool for generic chunks of memory
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- AllocOnlyPool<Branch> bpool; // pool for allocating Branches
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- AllocOnlyPool<RangeState> rpool; // pool for allocating RangeStates
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- AllocOnlyPool<Edit> epool; // pool for allocating Edits
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1730,7 +1730,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool quiet,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bool mate1,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t minCostAdjustment,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- ChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bowtieChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int *btCnt) :
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- RangeSourceDriver<TRangeSource>(true, minCostAdjustment),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- len_(0), mate1_(mate1),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Description: Renamed seqan::fill function calls to use seqan::resize.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- SeqAn 1.3 renamed seqan::fill() to seqan::resize().
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- SeqAn ticket: http://trac.seqan.de/ticket/77
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Forwarded: no
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Author: Ognyan Kulev <ogi@debian.org>
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-Last-Update: 2014-08-13
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- blockwise_sa.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ blockwise_sa.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -673,8 +673,8 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- try {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Allocate and initialize containers for holding bucket
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // sizes and representatives.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- fill(tparams[tid].bucketSzs, numBuckets, 0, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- fill(tparams[tid].bucketReps, numBuckets, OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ resize(tparams[tid].bucketSzs, numBuckets, 0, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ resize(tparams[tid].bucketReps, numBuckets, OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- } catch(bad_alloc &e) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if(this->_passMemExc) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- throw e; // rethrow immediately
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1063,7 +1063,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- hi = _sampleSuffs[cur_block];
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- //zHi.resizeExact(_dcV);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- //zHi.fillZero();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- fill(zHi, _dcV, 0, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ resize(zHi, _dcV, 0, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- assert_eq(getValue(zHi, 0), 0);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1074,7 +1074,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- lo = _sampleSuffs[cur_block-1];
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- //zLo.resizeExact(_dcV);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- //zLo.fillZero();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- fill(zLo, _dcV, 0, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ resize(zLo, _dcV, 0, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- assert_gt(_dcV, 3);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- assert_eq(getValue(zLo, 0), 0);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- calcZ(t, lo, zLo, this->verbose(), this->sanityCheck());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- diff_sample.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ diff_sample.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -457,7 +457,7 @@ static String<T> getDeltaMap(T v, const
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Declare anchor-map-related items
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- String<T> amap;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size_t amapEnts = 1;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- fill(amap, v, 0xffffffff, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ resize(amap, v, 0xffffffff, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- amap[0] = 0;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Print out difference cover (and optionally calculate
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // anchor map)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -540,7 +540,7 @@ public:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- assert_gt(_d, 0);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- assert_eq(1, popCount(_v)); // must be power of 2
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Build map from d's to idx's
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- fill(_dInv, _v, 0xffffffff, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ resize(_dInv, _v, 0xffffffff, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t lim = (uint32_t)length(_ds);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for(uint32_t i = 0; i < lim; i++) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- _dInv[_ds[i]] = i;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -664,7 +664,7 @@ void DifferenceCoverSample<TStr>::doBuil
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- VMSG_NL(" Doing sanity check");
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- TIndexOffU added = 0;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- String<TIndexOffU> sorted;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- fill(sorted, length(_isaPrime), OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ resize(sorted, length(_isaPrime), OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for(size_t di = 0; di < this->d(); di++) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- uint32_t d = _ds[di];
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size_t i = 0;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -728,7 +728,7 @@ void DifferenceCoverSample<TStr>::buildS
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- assert_eq(length(_doffs), d+1);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Size sPrime appropriately
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- reserve(sPrime, sPrimeSz + padding, Exact()); // reserve extra slot for LS
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- fill(sPrime, sPrimeSz + padding, OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ resize(sPrime, sPrimeSz + padding, OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // Slot suffixes from text into sPrime according to the mu
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // mapping; where the mapping would leave a blank, insert a 0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- TIndexOffU added = 0;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -952,7 +952,7 @@ void DifferenceCoverSample<TStr>::build(
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // arrays back into sPrime.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- VMSG_NL(" Allocating rank array");
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- reserve(_isaPrime, length(sPrime), Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- fill(_isaPrime, length(sPrime), OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ resize(_isaPrime, length(sPrime), OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- assert_gt(length(_isaPrime), 0);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- Timer timer(cout, " Ranking v-sort output time: ", this->verbose());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- Makefile.orig 2017-12-12 11:29:54.000000000 -0700
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ Makefile 2019-01-27 04:46:19.000000000 -0700
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -7,10 +7,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- prefix ?= /usr/local
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bindir = $(prefix)/bin
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--SEQAN_DIR = ./SeqAn-1.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--# treat SeqAn as a sysdir to suppress warnings
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--SEQAN_INC = -isystem $(SEQAN_DIR)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- CXX ?= g++
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- CPP ?= $(CXX)
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- CC ?= gcc
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -178,7 +175,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- $(wildcard genomes/NC_008253.fna) \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- $(wildcard reads/e_coli_1000.*) \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- $(wildcard reads/e_coli_1000_*) \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- SeqAn-1.1 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie-build \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- bowtie-inspect \
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