<pre style='margin:0'>
Marcus Calhoun-Lopez (MarcusCalhoun-Lopez) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/190e52cb3c29a34055f14087cb21889290c04680">https://github.com/macports/macports-ports/commit/190e52cb3c29a34055f14087cb21889290c04680</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit 190e52cb3c29a34055f14087cb21889290c04680
</span>Author: Marcus Calhoun-Lopez <mcalhoun@macports.org>
AuthorDate: Sun Jan 27 19:10:20 2019 -0700
<span style='display:block; white-space:pre;color:#404040;'> bowtie: use MacPorts version of SeqAn
</span>---
science/bowtie/Portfile | 8 +-
science/bowtie/files/patch-Makefile.diff | 24 +-
science/bowtie/files/patch-seqan.diff | 559 +++++++++++++++++++++++++++++++
3 files changed, 582 insertions(+), 9 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 c7924ca..09918f7 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;'>@@ -5,7 +5,7 @@ PortGroup github 1.0
</span>
name bowtie
github.setup BenLangmead bowtie 1.2.2_p1 v
<span style='display:block; white-space:pre;background:#ffe0e0;'>-revision 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 1
</span> categories science biology
platforms darwin
maintainers {mcalhoun @MarcusCalhoun-Lopez} openmaintainer
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -26,16 +26,20 @@ checksums rmd160 9f818e1e85abaf09ddc58cbe96f9cf735f0ca918 \
</span> sha256 ed1581d6ed97271e6de2c1f826a3169f1d5495461cd6f31b2b8f02e5e4adeebf \
size 7890653
<span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles-append patch-Makefile.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles-append patch-Makefile.diff \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patch-seqan.diff
</span>
supported_archs x86_64 ppc64
installs_libs no
<span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_build-append port:seqan-1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> depends_lib-append port:zlib \
port:tbb
# replicate values from Makefile prior to patching
configure.optflags -O3
<span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.cppflags-prepend -I${prefix}/include/seqan-1
</span>
configure.cmd printenv
configure.pre_args
<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 73d91e3..e30eab1 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;'>@@ -1,6 +1,6 @@
</span> --- Makefile.orig 2017-12-12 11:29:54.000000000 -0700
<span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ Makefile 2019-01-19 07:51:44.000000000 -0700
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2,16 +2,17 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ Makefile 2019-01-27 04:52:46.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2,16 +2,18 @@
</span> # Makefile for bowtie, bowtie-build, bowtie-inspect
#
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -11,9 +11,8 @@
</span> bindir = $(prefix)/bin
SEQAN_DIR = ./SeqAn-1.1
<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;'>-+SEQAN_INC = -I $(SEQAN_DIR)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # treat SeqAn as a sysdir to suppress warnings
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SEQAN_INC = -isystem $(SEQAN_DIR)
</span> INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
-CPP = g++
-CXX = $(CPP)
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -24,7 +23,18 @@
</span> LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
HEADERS = $(wildcard *.h)
BOWTIE_MM = 1
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -49,14 +50,6 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -19,8 +21,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ EXTRA_FLAGS =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ EXTRA_CFLAGS =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ EXTRA_CXXFLAGS =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-CFLAGS += $(EXTRA_CFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-CXXFLAGS += $(EXTRA_CXXFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++CFLAGS += $(EXTRA_CFLAGS) $(CPPFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++CXXFLAGS += $(EXTRA_CXXFLAGS) $(CPPFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ WARNING_FLAGS = -Wall -Wno-unused-parameter -Wno-reorder \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ -Wno-unused-local-typedefs
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -49,14 +51,6 @@
</span> MACOS =
ifneq (,$(findstring Darwin,$(shell uname)))
MACOS = 1
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -39,7 +49,7 @@
</span> endif
LINUX =
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -159,29 +152,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -159,29 +153,8 @@
</span> SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
VERSION = $(shell cat VERSION)
<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>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..dca0f99
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bowtie/files/patch-seqan.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,559 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Description: Change class name of _Context_LSS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ New version 1.4 of SeQan uses a different name of the class.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Forwarded: no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Author: Gert Wollny <gw.fossdev@gmail.com>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Last-Update: 2014-100-06
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- diff_sample.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ diff_sample.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -979,7 +979,7 @@ void DifferenceCoverSample<TStr>::build(
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Timer timer(cout, " Invoking Larsson-Sadakane on ranks time: ", this->verbose());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ VMSG_NL(" Invoking Larsson-Sadakane on ranks");
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- _Context_LSS<TIndexOff> c;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ ContextLss_<TIndexOff> c;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ c.suffixsort(
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ (TIndexOff*)begin(_isaPrime, Standard()),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ (TIndexOff*)begin(sPrime, Standard()),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Description: Proper type-casting in using seqan::_setBegin().
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Required by newer versions of GCC.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Forwarded: no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Author: Ognyan Kulev <ogi@debian.org>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Last-Update: 2013-04-18
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- pat.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ pat.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -120,13 +120,13 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ~Read() {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ clearAll(); reset();
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Prevent seqan from trying to free buffers
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- _setBegin(patFw, NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- _setBegin(patRc, NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- _setBegin(qual, NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- _setBegin(patFwRev, NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- _setBegin(patRcRev, NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- _setBegin(qualRev, NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- _setBegin(name, NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ _setBegin(patFw, (Dna5*)NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ _setBegin(patRc, (Dna5*)NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ _setBegin(qual, (char*)NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ _setBegin(patFwRev, (Dna5*)NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ _setBegin(patRcRev, (Dna5*)NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ _setBegin(qualRev, (char*)NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ _setBegin(name, (char*)NULL);
</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;'>+ #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:#e0ffe0;'>+Description: Use SeqAn 1.4's seqan::popCount() function instead of own function
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Author: Ognyan Kulev <ogi@debian.org>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Last-Update: 2014-03-08
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+---
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- diff_sample.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ diff_sample.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -481,6 +481,8 @@ static String<T> getDeltaMap(T v, const
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ return amap;
</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;'>++// Debian: Use seqan::popCount
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#if 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ /**
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ * Return population count (count of all bits set to 1) of i.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ */
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -493,6 +495,7 @@ static unsigned int popCount(T i) {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ return cnt;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#endif
</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;'>+ * Calculate log-base-2 of i
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Description: Renamed ChunkPool class to bowtieChunkPool.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SeqAn has a class with the same name and fatal name collision happens.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Forwarded: no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Author: Ognyan Kulev <ogi@debian.org>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Last-Update: 2013-04-18
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- aligner.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ aligner.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -391,7 +391,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool verbose,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool quiet,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int maxBts,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int *btCnt = NULL,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ AlignerMetrics *metrics = NULL) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Aligner(true, rangeMode),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -597,7 +597,7 @@ protected:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool quiet_; // don't print informational/warning info
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const int maxBts_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int *btCnt_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ AlignerMetrics *metrics_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ };
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -638,7 +638,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool verbose,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool quiet,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int maxBts,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int *btCnt) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Aligner(true, rangeMode),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ refs_(refs),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1405,7 +1405,7 @@ protected:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool quiet_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int maxBts_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int *btCnt_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Range-finding state for first mate
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1529,7 +1529,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool verbose,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool quiet,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int maxBts,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int *btCnt) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Aligner(true, rangeMode),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ refs_(refs),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2076,7 +2076,7 @@ protected:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ TDriver* driver_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Pool for distributing chunks of best-first path descriptor memory
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool verbose_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool quiet_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- aligner_0mm.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ aligner_0mm.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -32,7 +32,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache* cacheFw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache* cacheBw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool maqPenalty,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -123,7 +123,7 @@ private:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool maqPenalty_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -162,7 +162,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache* cacheFw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache* cacheBw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool reportSe,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -363,7 +363,7 @@ private:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const bool reportSe_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- aligner_1mm.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ aligner_1mm.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -32,7 +32,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool maqPenalty,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -160,7 +160,7 @@ private:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const bool maqPenalty_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -199,7 +199,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool reportSe,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -475,7 +475,7 @@ private:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const bool reportSe_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- aligner_23mm.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ aligner_23mm.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -33,7 +33,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool maqPenalty,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -230,7 +230,7 @@ private:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const bool maqPenalty_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -271,7 +271,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool reportSe,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -672,7 +672,7 @@ private:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const bool reportSe_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- aligner_seed_mm.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ aligner_seed_mm.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -37,7 +37,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache* cacheFw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache* cacheBw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool maqPenalty,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -554,7 +554,7 @@ private:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool strandFix_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -598,7 +598,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache* cacheFw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache* cacheBw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t cacheLimit,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool reportSe,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1375,7 +1375,7 @@ private:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheFw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeCache *cacheBw_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const uint32_t cacheLimit_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ BitPairReference* refs_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ vector<String<Dna5> >& os_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const bool reportSe_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- ebwt_search.cpp
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ ebwt_search.cpp
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -125,7 +125,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ static bool strandFix; // attempt to fix strand bias
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ static bool stats; // print performance stats
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ static int chunkPoolMegabytes; // max MB to dedicate to best-first search frames per thread
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-static int chunkSz; // size of single chunk disbursed by ChunkPool
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++static int chunkSz; // size of single chunk disbursed by bowtieChunkPool
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ static bool chunkVerbose; // have chunk allocator output status messages?
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ static bool useV1;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ static bool reportSe;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -232,7 +232,7 @@ norc = false; // don't align rc orientation of read
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ strandFix = true; // attempt to fix strand bias
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ stats = false; // print performance stats
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- chunkSz = 256; // size of single chunk disbursed by ChunkPool (in KB)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ chunkSz = 256; // size of single chunk disbursed by bowtieChunkPool (in KB)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ chunkVerbose = false; // have chunk allocator output status messages?
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ useV1 = true;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reportSe = false;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1340,7 +1340,7 @@ static void exactSearchWorkerStateful(vo
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ UnpairedExactAlignerV1Factory alSEfact(
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ebwt,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ NULL,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1629,7 +1629,7 @@ static void mismatchSearchWorkerFullStat
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Global initialization
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Unpaired1mmAlignerV1Factory alSEfact(
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ebwtFw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2080,7 +2080,7 @@ static void twoOrThreeMismatchSearchWork
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Unpaired23mmAlignerV1Factory alSEfact(
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ebwtFw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ &ebwtBw,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2750,7 +2750,7 @@ static void seededQualSearchWorkerFullSt
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Global initialization
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *pool = new ChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *pool = new bowtieChunkPool(chunkSz * 1024, chunkPoolMegabytes * 1024 * 1024, chunkVerbose);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ AlignerMetrics *metrics = NULL;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if(stats) {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- ebwt_search_backtrack.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ ebwt_search_backtrack.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2703,7 +2703,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool verbose,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool quiet,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool mate1,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int *btCnt) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SingleRangeSourceDriver<EbwtRangeSource>(
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ params, rs, fw, sink, sinkPt, os, verbose,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2877,7 +2877,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool verbose,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool quiet,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool mate1,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int *btCnt = NULL) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ params_(params),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ rs_(rs),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2936,7 +2936,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool verbose_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool quiet_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool mate1_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool* pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool* pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int *btCnt_;
</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;'>+--- pool.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ pool.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -19,13 +19,13 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ * is set at construction time. Heap memory is only allocated at
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ * construction and deallocated at destruction.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ */
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-class ChunkPool {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++class bowtieChunkPool {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ /**
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ * Initialize a new pool with an initial size of about 'bytes'
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ * bytes. Exit with an error message if we can't allocate it.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ */
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool(uint32_t chunkSz, uint32_t totSz, bool verbose_) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ verbose(verbose_), patid(0), pool_(NULL), cur_(0),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bits_(lim_), exhaustCrash_(false),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -38,7 +38,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ } catch(std::bad_alloc& e) {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ThreadSafe _ts(&gLock);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- std::cerr << "Error: Could not allocate ChunkPool of "
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ std::cerr << "Error: Could not allocate bowtieChunkPool of "
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ << totSz << " bytes" << std::endl;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ exhausted();
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ throw 1; // Exit if we haven't already
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -48,7 +48,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ /**
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ * Delete all the pools.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ */
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ~ChunkPool() {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ ~bowtieChunkPool() {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if(pool_ != NULL) delete[] pool_;
</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;'>+@@ -189,7 +189,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ * Initialize a new pool with an initial size of about 'bytes'
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ * bytes. Exit with an error message if we can't allocate it.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ */
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- AllocOnlyPool(ChunkPool* pool, const char *name) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ AllocOnlyPool(bowtieChunkPool* pool, const char *name) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ pool_(pool), name_(name), curPool_(0), cur_(0)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ assert(pool != NULL);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -388,7 +388,7 @@ protected:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ lastCurInPool_.pop_back();
</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;'>+- ChunkPool* pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool* pool_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const char *name_;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ std::vector<T*> pools_; /// the memory pools
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t curPool_; /// pool we're current allocating from
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- range_source.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ range_source.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1307,7 +1307,7 @@ class PathManager {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- PathManager(ChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ PathManager(bowtieChunkPool* cpool_, int *btCnt, bool verbose, bool quiet) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ branchQ_(verbose, quiet),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ cpool(cpool_),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bpool(cpool, "branch"),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1556,7 +1556,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool *cpool; // pool for generic chunks of memory
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool *cpool; // pool for generic chunks of memory
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ AllocOnlyPool<Branch> bpool; // pool for allocating Branches
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ AllocOnlyPool<RangeState> rpool; // pool for allocating RangeStates
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ AllocOnlyPool<Edit> epool; // pool for allocating Edits
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1730,7 +1730,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool quiet,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bool mate1,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t minCostAdjustment,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- ChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ bowtieChunkPool* pool,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ int *btCnt) :
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RangeSourceDriver<TRangeSource>(true, minCostAdjustment),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ len_(0), mate1_(mate1),
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Description: Renamed seqan::fill function calls to use seqan::resize.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SeqAn 1.3 renamed seqan::fill() to seqan::resize().
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ SeqAn ticket: http://trac.seqan.de/ticket/77
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Forwarded: no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Author: Ognyan Kulev <ogi@debian.org>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+Last-Update: 2014-08-13
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- blockwise_sa.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ blockwise_sa.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -665,8 +665,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ try {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Allocate and initialize containers for holding bucket
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // sizes and representatives.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- fill(tparams[tid].bucketSzs, numBuckets, 0, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- fill(tparams[tid].bucketReps, numBuckets, OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ resize(tparams[tid].bucketSzs, numBuckets, 0, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ resize(tparams[tid].bucketReps, numBuckets, OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ } catch(bad_alloc &e) {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ if(this->_passMemExc) {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ throw e; // rethrow immediately
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1055,7 +1055,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ hi = _sampleSuffs[cur_block];
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ //zHi.resizeExact(_dcV);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ //zHi.fillZero();
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- fill(zHi, _dcV, 0, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ resize(zHi, _dcV, 0, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ assert_eq(getValue(zHi, 0), 0);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1066,7 +1066,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ lo = _sampleSuffs[cur_block-1];
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ //zLo.resizeExact(_dcV);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ //zLo.fillZero();
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- fill(zLo, _dcV, 0, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ resize(zLo, _dcV, 0, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ assert_gt(_dcV, 3);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ assert_eq(getValue(zLo, 0), 0);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ calcZ(t, lo, zLo, this->verbose(), this->sanityCheck());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- diff_sample.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ diff_sample.h
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -457,7 +457,7 @@ static String<T> getDeltaMap(T v, const
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Declare anchor-map-related items
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ String<T> amap;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size_t amapEnts = 1;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- fill(amap, v, 0xffffffff, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ resize(amap, v, 0xffffffff, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ amap[0] = 0;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Print out difference cover (and optionally calculate
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // anchor map)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -540,7 +540,7 @@ public:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ assert_gt(_d, 0);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ assert_eq(1, popCount(_v)); // must be power of 2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Build map from d's to idx's
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- fill(_dInv, _v, 0xffffffff, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ resize(_dInv, _v, 0xffffffff, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t lim = (uint32_t)length(_ds);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ for(uint32_t i = 0; i < lim; i++) {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ _dInv[_ds[i]] = i;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -664,7 +664,7 @@ void DifferenceCoverSample<TStr>::doBuil
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ VMSG_NL(" Doing sanity check");
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ TIndexOffU added = 0;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ String<TIndexOffU> sorted;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- fill(sorted, length(_isaPrime), OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ resize(sorted, length(_isaPrime), OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ for(size_t di = 0; di < this->d(); di++) {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ uint32_t d = _ds[di];
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size_t i = 0;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -728,7 +728,7 @@ void DifferenceCoverSample<TStr>::buildS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ assert_eq(length(_doffs), d+1);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Size sPrime appropriately
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reserve(sPrime, sPrimeSz + padding, Exact()); // reserve extra slot for LS
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- fill(sPrime, sPrimeSz + padding, OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ resize(sPrime, sPrimeSz + padding, OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // Slot suffixes from text into sPrime according to the mu
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // mapping; where the mapping would leave a blank, insert a 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ TIndexOffU added = 0;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -952,7 +952,7 @@ void DifferenceCoverSample<TStr>::build(
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ // arrays back into sPrime.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ VMSG_NL(" Allocating rank array");
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ reserve(_isaPrime, length(sPrime), Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- fill(_isaPrime, length(sPrime), OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ resize(_isaPrime, length(sPrime), OFF_MASK, Exact());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ assert_gt(length(_isaPrime), 0);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Timer timer(cout, " Ranking v-sort output time: ", this->verbose());
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- Makefile.orig 2017-12-12 11:29:54.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ Makefile 2019-01-27 04:46:19.000000000 -0700
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -7,10 +7,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ prefix ?= /usr/local
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bindir = $(prefix)/bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-SEQAN_DIR = ./SeqAn-1.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# treat SeqAn as a sysdir to suppress warnings
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-SEQAN_INC = -isystem $(SEQAN_DIR)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ CXX ?= g++
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ CPP ?= $(CXX)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ CC ?= gcc
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -178,7 +175,6 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ $(wildcard genomes/NC_008253.fna) \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ $(wildcard reads/e_coli_1000.*) \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ $(wildcard reads/e_coli_1000_*) \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- SeqAn-1.1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bowtie \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bowtie-build \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bowtie-inspect \
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</pre>