CMakeLists.txt

@@ -5,8 +5,6 @@ option(BUILD_STATIC "BUILD_STATIC" OFF)
 option(EXTRA "EXTRA" OFF)
 option(STATIC_LIBGCC "STATIC_LIBGCC" OFF)
 option(STATIC_LIBSTDC++ "STATIC_LIBSTDC++" OFF)
-option(SSSE3 "SSSE3" OFF)
-option(POPCNT "POPCNT" OFF)
 
 IF(STATIC_LIBSTDC++)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libstdc++")
@@ -29,19 +27,8 @@ else()
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=gnu++11")
 endif()
 
-if(SSSE3)
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mssse3")
-  if(POPCNT)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt")
-  endif()
-elseif(CMAKE_BUILD_MARCH)
+if(CMAKE_BUILD_MARCH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${CMAKE_BUILD_MARCH}")
-else()
-  include(CheckCXXCompilerFlag)
-  CHECK_CXX_COMPILER_FLAG("-march=native" COMPILER_SUPPORTS_MARCHNATIVE)
-  if(COMPILER_SUPPORTS_MARCHNATIVE)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
-  endif()
 endif()
 
 find_package(ZLIB REQUIRED)
@@ -52,7 +39,7 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
 endif()
 
 if(WIN32)
-  add_definitions(-D_CRT_SECURE_NO_WARNINGS)
+  add_definitions(-D_CRT_SECURE_NO_WARNINGS -D_ITERATOR_DEBUG_LEVEL=0)
 else()
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable")
 endif()
@@ -61,7 +48,25 @@ include_directories(
   "${CMAKE_SOURCE_DIR}/src"
   "${ZLIB_INCLUDE_DIR}")
 
-add_executable(diamond src/run/main.cpp
+set(DISPATCH_OBJECTS
+"src/dp/swipe/banded_3frame_swipe.cpp"
+"src/dp/swipe/swipe.cpp"
+"src/dp/swipe/banded_swipe.cpp"
+"src/search/collision.cpp"
+"src/search/stage1.cpp"
+"src/search/stage2.cpp"
+"src/tools/benchmark.cpp"
+"src/dp/swipe/swipe_wrapper.cpp"
+)
+
+add_library(arch_generic OBJECT ${DISPATCH_OBJECTS})
+target_compile_options(arch_generic PUBLIC -DDISPATCH_ARCH=ARCH_GENERIC)
+add_library(arch_sse4_1 OBJECT ${DISPATCH_OBJECTS})
+target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1 -mssse3 -mpopcnt -msse4.1)
+
+add_executable(diamond $<TARGET_OBJECTS:arch_generic>
+  $<TARGET_OBJECTS:arch_sse4_1>
+  src/run/main.cpp
   src/basic/config.cpp
   src/basic/score_matrix.cpp
   src/blast/blast_filter.cpp
@@ -78,7 +83,6 @@ add_executable(diamond src/run/main.cpp
   src/data/reference.cpp
   src/data/seed_histogram.cpp
   src/output/daa_record.cpp
-  src/search/search.cpp
   src/util/command_line_parser.cpp
   src/util/seq_file_format.cpp
   src/util/util.cpp 
@@ -88,7 +92,6 @@ add_executable(diamond src/run/main.cpp
   src/dp/ungapped_align.cpp
   src/run/tools.cpp
   src/dp/greedy_align.cpp
-  src/search/stage2.cpp
   src/output/output_format.cpp
   src/output/join_blocks.cpp
   src/data/frequent_seeds.cpp
@@ -99,7 +102,6 @@ add_executable(diamond src/run/main.cpp
   src/output/blast_pairwise_format.cpp
   src/dp/comp_based_stats.cpp
   src/run/double_indexed.cpp
-  src/search/collision.cpp
   src/output/sam_format.cpp
   src/align/align.cpp
   src/search/setup.cpp
@@ -107,9 +109,7 @@ add_executable(diamond src/run/main.cpp
   src/data/taxonomy.cpp
   src/lib/tantan/tantan.cc
   src/basic/masking.cpp
-  src/dp/swipe/swipe.cpp
   src/dp/banded_sw.cpp
-  src/data/sorted_list.cpp
   src/data/seed_set.cpp
   src/util/simd.cpp
   src/output/taxon_format.cpp
@@ -118,8 +118,6 @@ add_executable(diamond src/run/main.cpp
   src/output/target_culling.cpp
   src/align/greedy_pipeline.cpp
   src/align/swipe_pipeline.cpp
-  src/dp/swipe/banded_3frame_swipe.cpp
-  src/dp/swipe/banded_swipe.cpp
   src/align/banded_swipe_pipeline.cpp
   src/data/ref_dictionary.cpp
   src/util/io/compressed_stream.cpp
@@ -137,7 +135,6 @@ add_executable(diamond src/run/main.cpp
   src/data/taxonomy_nodes.cpp
   src/util/algo/MurmurHash3.cpp
   src/search/stage0.cpp
-  src/util/memory/memory_pool.cpp
   src/data/seed_array.cpp
   src/output/paf_format.cpp
   src/util/system/system.cpp
@@ -150,6 +147,7 @@ add_executable(diamond src/run/main.cpp
   src/util/system/getRSS.cpp
   src/util/math/sparse_matrix.cpp
   src/lib/tantan/LambdaCalculator.cc
+  src/data/taxonomy_filter.cpp
 )
 
 if(EXTRA)

README.md

@@ -18,7 +18,6 @@ Keep posted about new developments by following me on
 
 [![Build Status](https://travis-ci.org/bbuchfink/diamond.svg?branch=master)](https://travis-ci.org/bbuchfink/diamond)
 [![image](https://anaconda.org/bioconda/diamond/badges/version.svg)](https://anaconda.org/bioconda/diamond)
-![image](https://anaconda.org/bioconda/diamond/badges/platforms.svg)
 [![image](https://anaconda.org/bioconda/diamond/badges/downloads.svg)](https://anaconda.org/bioconda/diamond)
 
 Quick start guide
@@ -32,7 +31,7 @@ quick example for setting up and using the program on Linux.
 Installing the software on your system may be done by downloading it in
 binary format for immediate use:
 
-    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.26/diamond-linux64.tar.gz
+    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.28/diamond-linux64.tar.gz
     tar xzf diamond-linux64.tar.gz
 
 The extracted `diamond` binary file should be moved to a directory

build_simple.sh

@@ -82,4 +82,5 @@ g++ -std=gnu++11 -DNDEBUG -O3 -Wno-deprecated-declarations $1 $2 $3 \
   src/util/system/getRSS.cpp \
   src/util/math/sparse_matrix.cpp \
   src/lib/tantan/LambdaCalculator.cc \
+  src/data/taxonomy_filter.cpp \
 -lz -lpthread -o diamond

debian/changelog

+diamond-aligner (0.9.28+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * One patch against upstream could go (-mnative no longer set)
+
+ -- Steffen Moeller <moeller@debian.org>  Fri, 08 Nov 2019 19:28:00 +0100
+
 diamond-aligner (0.9.26+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -6,7 +6,7 @@ Priority: optional
 Build-Depends: debhelper-compat (= 12),
                cmake,
                zlib1g-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/diamond-aligner
 Vcs-Git: https://salsa.debian.org/med-team/diamond-aligner.git
 Homepage: https://github.com/bbuchfink/diamond

debian/patches/no_march_native.patch

-Description: Do not use march=native flag
-Bug-Debian: https://bugs.debian.org/906615
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Sun, 19 Aug 2018 06:38:58 +0200
-
-Index: diamond-aligner/CMakeLists.txt
-===================================================================
---- diamond-aligner.orig/CMakeLists.txt
-+++ diamond-aligner/CMakeLists.txt
-@@ -38,10 +38,10 @@ elseif(CMAKE_BUILD_MARCH)
-   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${CMAKE_BUILD_MARCH}")
- else()
-   include(CheckCXXCompilerFlag)
--  CHECK_CXX_COMPILER_FLAG("-march=native" COMPILER_SUPPORTS_MARCHNATIVE)
--  if(COMPILER_SUPPORTS_MARCHNATIVE)
--    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
--  endif()
-+  #CHECK_CXX_COMPILER_FLAG("-march=native" COMPILER_SUPPORTS_MARCHNATIVE)
-+  #if(COMPILER_SUPPORTS_MARCHNATIVE)
-+  #  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
-+  #endif()
- endif()
- 
- find_package(ZLIB REQUIRED)

debian/patches/series

 avoid_unwanted_optimisation.patch
-no_march_native.patch
 82feea2aee5c82e283704b9317cb5e8abc625f90.patch

src/ChangeLog

+[0.9.28]
+- Fixed a bug that could cause alignment score overflows for scores > 65535 in frameshift alignment mode.
+- Fixed a clang compiler error.
+
+[0.9.27]
+- Improved performance of the seed matching stage.
+- Seed frequency counts are computed based on hit seeds.
+- Added option `--taxon-exclude` to exclude list of taxon ids from search.
+- Compiling from source will no longer perform a native build. Instead, a portable binary that contains code paths
+  for multiple architectures will be produced, with dispatch logic that is invoked at runtime.
+
 [0.9.26]
 - Fixed a bug that could cause undefined behaviour when using a database file of format version < 2.
 - Fixed a compiler error when compiled as generic C++.

src/align/align.cpp

@@ -91,7 +91,7 @@ void align_worker(size_t thread_id, const Parameters *params, const Metadata *me
 		QueryMapper *mapper;
 		if (config.ext == Config::swipe)
 			mapper = new ExtensionPipeline::Swipe::Pipeline(*params, hits.query, hits.begin, hits.end);
-		else if (config.frame_shift != 0)
+		else if (config.frame_shift != 0 || config.ext == Config::banded_swipe)
 			mapper = new ExtensionPipeline::BandedSwipe::Pipeline(*params, hits.query, hits.begin, hits.end, dp_stat, hits.target_parallel);
 		else
 			mapper = new ExtensionPipeline::Greedy::Pipeline(*params, hits.query, hits.begin, hits.end);
@@ -142,7 +142,6 @@ void align_queries(Trace_pt_buffer &trace_pts, Consumer* output_file, const Para
 			threads.emplace_back(heartbeat_worker, query_range.second);
 		size_t n_threads = config.load_balancing == Config::query_parallel ? (config.threads_align == 0 ? config.threads_ : config.threads_align) : 1;
 		for (size_t i = 0; i < n_threads; ++i)
-			//threads.push_back(launch_thread(static_cast<void(*)(size_t)>(&align_worker), i));
 			threads.emplace_back(align_worker, i, &params, &metadata);
 		for (auto &t : threads)
 			t.join();

src/align/banded_swipe_pipeline.cpp

 /****
 DIAMOND protein aligner
-Copyright (C) 2013-2017 Benjamin Buchfink <buchfink@gmail.com>
+Copyright (C) 2013-2019 Benjamin Buchfink <buchfink@gmail.com>
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -20,6 +20,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "align.h"
 #include "../dp/dp.h"
 #include "../util/interval_partition.h"
+#include "../util/simd.h"
 
 using namespace std;
 
@@ -46,7 +47,7 @@ struct Target : public ::Target
 		return TranslatedPosition::absolute_interval(TranslatedPosition(i0, f), TranslatedPosition(i1, f), query_dna_len);
 	}
 
-	void add_strand(QueryMapper &mapper, vector<DpTarget> &v, vector<Seed_hit>::iterator begin, vector<Seed_hit>::iterator end)
+	void add_strand(QueryMapper &mapper, vector<DpTarget> &v, vector<Seed_hit>::iterator begin, vector<Seed_hit>::iterator end, int target_idx)
 	{
 		if (end == begin) return;
 		const int band = config.padding, d_min = -int(subject.length() - 1), d_max = int(mapper.query_seq(0).length() - 1);
@@ -58,15 +59,15 @@ struct Target : public ::Target
 				d1 = std::min(i->diagonal() + band, d_max);
 			}
 			else {
-				v.emplace_back(subject, d0, d1, &hsps, subject_id);
+				v.emplace_back(subject, d0, d1, target_idx);
 				d0 = std::max(i->diagonal() - band, d_min);
 				d1 = std::min(i->diagonal() + band, d_max);
 			}
 		}
-		v.emplace_back(subject, d0, d1, &hsps, subject_id);
+		v.emplace_back(subject, d0, d1, target_idx);
 	}
 
-	void add(QueryMapper &mapper, vector<DpTarget> &vf, vector<DpTarget> &vr)
+	void add(QueryMapper &mapper, vector<DpTarget> &vf, vector<DpTarget> &vr, int target_idx)
 	{
 		vector<Seed_hit>::iterator hits = mapper.seed_hits.begin() + begin, hits_end = mapper.seed_hits.begin() + end;
 		Strand strand = top_hit.strand();
@@ -77,9 +78,9 @@ struct Target : public ::Target
 
 		const auto it = find_if(hits, hits_end, [](const Seed_hit &x) { return x.strand() == REVERSE; });
 		if(strand == FORWARD || mapper.target_parallel)
-			add_strand(mapper, vf, hits, it);
+			add_strand(mapper, vf, hits, it, target_idx);
 		if (strand == REVERSE || mapper.target_parallel)
-			add_strand(mapper, vr, it, hits_end);
+			add_strand(mapper, vr, it, hits_end, target_idx);
 
 		//const int d = hits[0].diagonal();
 		//const DpTarget t(subject, std::max(d - 32, -int(subject.length() - 1)), std::min(d + 32, int(mapper.query_seq(0).length() - 1)), &hsps, subject_id);		
@@ -100,6 +101,10 @@ struct Target : public ::Target
 	void finish(QueryMapper &mapper)
 	{
 		inner_culling(mapper.raw_score_cutoff());
+		if (config.frame_shift)
+			return;
+		for (list<Hsp>::iterator i = hsps.begin(); i != hsps.end(); ++i)
+			i->query_source_range = TranslatedPosition::absolute_interval(TranslatedPosition(i->query_range.begin_, Frame(i->frame)), TranslatedPosition(i->query_range.end_, Frame(i->frame)), mapper.source_query_len);
 	}
 
 	bool is_outranked(const IntervalPartition &ip, int source_query_len, double rr) const
@@ -148,9 +153,18 @@ void Pipeline::run_swipe(bool score_only)
 {
 	vector<DpTarget> vf, vr;
 	for (size_t i = 0; i < n_targets(); ++i)
-		target(i).add(*this, vf, vr);
-	banded_3frame_swipe(translated_query, FORWARD, vf.begin(), vf.end(), this->dp_stat, score_only, target_parallel);
-	banded_3frame_swipe(translated_query, REVERSE, vr.begin(), vr.end(), this->dp_stat, score_only, target_parallel);
+		target(i).add(*this, vf, vr, (int)i);
+	if (score_matrix.frame_shift()) {
+		list<Hsp> hsp = banded_3frame_swipe(translated_query, FORWARD, vf.begin(), vf.end(), this->dp_stat, score_only, target_parallel);
+		hsp.splice(hsp.end(), banded_3frame_swipe(translated_query, REVERSE, vr.begin(), vr.end(), this->dp_stat, score_only, target_parallel));
+		while (!hsp.empty()) {
+			list<Hsp> &l = target(hsp.begin()->swipe_target).hsps;
+			l.splice(l.end(), hsp, hsp.begin());
+		}
+	}
+	else {
+		DP::BandedSwipe::swipe(query_seq(0), vf.begin(), vf.end(), Frame(0), score_only ? 0 : DP::TRACEBACK);
+	}
 }
 
 void build_ranking_worker(PtrVector<::Target>::iterator begin, PtrVector<::Target>::iterator end, Atomic<size_t> *next, vector<unsigned> *intervals) {

src/align/swipe_pipeline.cpp

@@ -25,14 +25,15 @@ namespace ExtensionPipeline { namespace Swipe {
 void Pipeline::run(Statistics &stat)
 {
 	const size_t n = targets.size();
-	vector<DpTarget> seqs(n);
+	vector<sequence> seqs(n);
 	for (size_t i = 0; i < n; ++i) {
-		seqs[i].seq = ref_seqs::get()[targets[i].subject_id];
+		seqs[i] = ref_seqs::get()[targets[i].subject_id];
 	}
-	vector<int> scores(n);
-	swipe(query_seq(0), seqs.begin(), seqs.end(), scores.begin());
-	for (size_t i = 0; i < n; ++i)
+	vector<int> scores = DP::Swipe::swipe(query_seq(0), seqs.data(), seqs.data() + seqs.size());
+	for (size_t i = 0; i < n; ++i) {
 		targets[i].hsps.push_back(Hsp(scores[i]));
+		targets[i].hsps.back().frame = 0;
+	}
 }
 
 }}
\ No newline at end of file

src/basic/basic.cpp

@@ -24,7 +24,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "sequence.h"
 #include "masking.h"
 
-const char* Const::version_string = "0.9.26";
+const char* Const::version_string = "0.9.28";
 const char* Const::program_name = "diamond";
 const char* Const::id_delimiters = " \a\b\f\n\r\t\v\1";
 

src/basic/config.cpp

@@ -28,11 +28,11 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "shape_config.h"
 #include "../util/io/temp_file.h"
 #include "../basic/match.h"
-#include "../data/sorted_list.h"
 #include "../basic/translate.h"
 #include "../dp/dp.h"
 #include "masking.h"
 #include "../util/system/system.h"
+#include "../util/simd.h"
 
 using namespace std;
 
@@ -72,7 +72,9 @@ Config::Config(int argc, const char **argv)
 		.add_command("cluster", "")
 		.add_command("translate", "")
 		.add_command("filter-blasttab", "")
-		.add_command("show-cbs", "");
+		.add_command("show-cbs", "")
+		.add_command("simulate-seqs", "")
+		.add_command("split", "");
 
 	Options_group general("General options");
 	general.add()
@@ -171,7 +173,8 @@ Config::Config(int argc, const char **argv)
 		("taxonmap", 0, "protein accession to taxid mapping file", prot_accession2taxid)
 		("taxonnodes", 0, "taxonomy nodes.dmp from NCBI", nodesdmp)
 		("taxonnames", 0, "taxonomy names.dmp from NCBI", namesdmp)
-		("taxonlist", 0, "restrict search to list of taxon ids (comma-separated)", taxonlist);
+		("taxonlist", 0, "restrict search to list of taxon ids (comma-separated)", taxonlist)
+		("taxon-exclude", 0, "exclude list of taxon ids (comma-separated)", taxon_exclude);
 
 	Options_group advanced("Advanced options");
 	advanced.add()
@@ -266,7 +269,6 @@ Config::Config(int argc, const char **argv)
 		("join-split-key-len", 0, "", join_split_key_len, 17u)
 		("radix-bits", 0, "", radix_bits, 8u)
 		("join-ht-factor", 0, "", join_ht_factor, 1.3)
-		("hash-join", 0, "", hash_join)
 		("sort-join", 0, "", sort_join)
 		("simple-freq", 0, "", simple_freq)
 		("freq-treshold", 0, "", freq_treshold)
@@ -428,7 +430,7 @@ Config::Config(int argc, const char **argv)
 		
 		init_cbs();
 		raw_ungapped_xdrop = score_matrix.rawscore(ungapped_xdrop);
-		simd_messages();
+		verbose_stream << "CPU features detected: " << SIMD::features() << endl;
 	}
 
 	Translator::init(query_gencode);

src/basic/config.h

@@ -155,7 +155,6 @@ struct Config
 	unsigned join_split_key_len;
 	unsigned radix_bits;
 	double join_ht_factor;
-	bool hash_join;
 	bool sort_join;
 	bool simple_freq;
 	double freq_treshold;
@@ -181,11 +180,12 @@ struct Config
 	int stop_match_score;
 	int tantan_maxRepeatOffset;
 	bool tantan_ungapped;
+	string taxon_exclude;
 
 	enum {
 		makedb = 0, blastp = 1, blastx = 2, view = 3, help = 4, version = 5, getseq = 6, benchmark = 7, random_seqs = 8, compare = 9, sort = 10, roc = 11, db_stat = 12, model_sim = 13,
 		match_file_stat = 14, model_seqs = 15, opt = 16, mask = 17, fastq2fasta = 18, dbinfo = 19, test_extra = 20, test_io = 21, db_annot_stats = 22, read_sim = 23, info = 24, seed_stat = 25,
-		smith_waterman = 26, protein_snps = 27, cluster = 28, translate = 29, filter_blasttab = 30, show_cbs = 31
+		smith_waterman = 26, protein_snps = 27, cluster = 28, translate = 29, filter_blasttab = 30, show_cbs = 31, simulate_seqs = 32, split = 33
 	};
 	unsigned	command;
 

src/basic/const.h

@@ -23,7 +23,7 @@ struct Const
 {
 
 	enum {
-		build_version = 127,
+		build_version = 129,
 		seedp_bits = 10,
 		seedp = 1<<seedp_bits,
 		max_seed_weight = 32,

src/basic/match.h

@@ -206,7 +206,7 @@ struct Hsp
 
 	bool is_weakly_enveloped(const Hsp &j) const;
 	std::pair<int, int> diagonal_bounds() const;
-	unsigned score, frame, length, identities, mismatches, positives, gap_openings, gaps, sw_score;
+	unsigned score, frame, length, identities, mismatches, positives, gap_openings, gaps, sw_score, swipe_target;
 	float time;
 	interval query_source_range, query_range, subject_range;
 	Packed_transcript transcript;

src/basic/reduction.h

@@ -41,7 +41,8 @@ struct Reduction
 		map_[(long)Translator::STOP] = value_traits.mask_char;
 		const vector<string> tokens(tokenize(definition_string, " "));
 		size_ = (unsigned)tokens.size();
-		bit_size_ = (uint64_t)ceil(log(size_) / log(2));
+		bit_size_exact_ = log(size_) / log(2);
+		bit_size_ = (uint64_t)ceil(bit_size_exact_);
 		for (unsigned i = 0; i<size_; ++i)
 			for (unsigned j = 0; j<tokens[i].length(); ++j) {
 				const char ch = tokens[i][j];
@@ -61,6 +62,10 @@ struct Reduction
 		return bit_size_;
 	}
 
+	double bit_size_exact() const {
+		return bit_size_exact_;
+	}
+
 	unsigned operator()(Letter a) const
 	{
 		return map_[(long)a];
@@ -108,6 +113,7 @@ private:
 #endif
 	unsigned size_;
 	uint64_t bit_size_;
+	double bit_size_exact_;
 
 };
 

src/basic/score_matrix.cpp

@@ -36,7 +36,7 @@ typedef double array_of_8[BLAST_NUM_STAT_VALUES];
 
 const double INT2_MAX = std::numeric_limits<double>::max();
 
-const char DNA_scores[5 * 5] = {
+const signed char DNA_scores[5 * 5] = {
 	2, -3, -3, -3, -3,
 	-3,2,-3,-3,-3,
 	-3,-3,2,-3,-3,

src/basic/shape.h

@@ -134,7 +134,6 @@ struct Shape
 		for (unsigned i = 0; i < weight_; ++i) {
 			Letter l = seq[positions_[i]];
 			if (l == value_traits.mask_char || l == sequence::DELIMITER || l == Translator::STOP)
-			//if (l == value_traits.mask_char || l == sequence::DELIMITER)
 				return false;
 			unsigned r = Reduction::reduction(l);
 #ifdef FREQUENCY_MASKING
@@ -156,7 +155,6 @@ struct Shape
 		for (unsigned i = 0; i < weight_; ++i) {
 			Letter l = seq[positions_[i]];
 			if (l == value_traits.mask_char || l == sequence::DELIMITER || l == Translator::STOP)
-			//if (l == value_traits.mask_char || l == sequence::DELIMITER)
 				return false;
 			unsigned r = Reduction::reduction(l);
 			s <<= b;

src/basic/statistics.h

@@ -24,7 +24,6 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <string.h>
 #include <mutex>
 #include "../util/log_stream.h"
-#include "../util/memory/memory_pool.h"
 
 typedef uint64_t stat_type;
 
@@ -94,7 +93,6 @@ struct Statistics
 		log_stream << "MSE = " << (double)data_[SQUARED_ERROR] / (double)data_[OUT_HITS] << endl;
 		//log_stream << "Cells = " << data_[CELLS] << endl;
 		verbose_stream << "Temporary disk space used: " << (double)data_[TEMP_SPACE] / (1 << 30) << " GB" << endl;
-		log_stream << "Memory pool maximum allocation size: " << (double)MemoryPool::global().max_alloc_size() / (1 << 30) << " GB" << endl;
 		log_stream << "Outranked hits = " << data_[OUTRANKED_HITS] << " (" << data_[OUTRANKED_HITS]*100.0/ data_[PAIRWISE] << "%)" << endl;
 		message_stream << "Reported " << data_[PAIRWISE] << " pairwise alignments, " << data_[MATCHES] << " HSPs." << endl;
 		message_stream << data_[ALIGNED] << " queries aligned." << endl;