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|
Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: save resources by not making/testing the -fsantize variants
--- a/Makefile
+++ b/Makefile
@@ -189,15 +189,6 @@ BUILD_CPPS_MAIN := $(BUILD_CPPS) bowtie_
SEARCH_FRAGMENTS := $(wildcard search_*_phase*.c)
VERSION := $(shell cat BOWTIE2_VERSION)
-SANITIZER_FLAGS :=
-ifeq (0,$(shell $(CXX) -E -fsanitize=address,undefined btypes.h > /dev/null 2>&1; echo $$?))
- SANITIZER_FLAGS := -fsanitize=address,undefined
-else ifeq (0,$(shell $(CXX) -E -fsanitize=address btypes.h > /dev/null 2>&1; echo $$?))
- SANITIZER_FLAGS := -fsanitize=address
-else ifeq (0,$(shell $(CXX) -E -fsanitize=undefined btypes.h > /dev/null 2>&1; echo $$?))
- SANITIZER_FLAGS := -fsanitize=undefined
-endif
-
DEBUG_FLAGS := -O0 -g3 $(SSE_FLAG)
RELEASE_FLAGS := -O3 $(SSE_FLAG) -funroll-loops -g3
NOASSERT_FLAGS := -DNDEBUG
@@ -217,15 +208,6 @@ BOWTIE2_BIN_LIST_DBG := bowtie2-build-s-
bowtie2-align-l-debug \
bowtie2-inspect-s-debug \
bowtie2-inspect-l-debug
-BOWTIE2_BIN_LIST_SAN := bowtie2-build-s-sanitized \
- bowtie2-build-l-sanitized \
- bowtie2-align-s-sanitized \
- bowtie2-align-l-sanitized \
- bowtie2-inspect-s-sanitized \
- bowtie2-inspect-l-sanitized
-ifndef SANITIZER_FLAGS
- BOWTIE2_BIN_LIST_SAN =
-endif
GENERAL_LIST := $(wildcard scripts/*.sh) \
$(wildcard scripts/*.pl) \
@@ -277,10 +259,9 @@ endif
.PHONY: all allall both both-debug
all: $(BOWTIE2_BIN_LIST) ;
-allall: $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) $(BOWTIE2_BIN_LIST_SAN) ;
+allall: $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) ;
both: bowtie2-align-s bowtie2-build-s bowtie2-align-l bowtie2-build-l ;
both-debug: bowtie2-align-s-debug bowtie2-build-s-debug bowtie2-align-l-debug bowtie2-build-l-debug ;
-both-sanitized: bowtie2-align-s-sanitized bowtie2-build-s-sanitized bowtie2-align-l-sanitized bowtie2-build-l-sanitized ;
DEFS := -fno-strict-aliasing \
-DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" \
@@ -294,18 +275,11 @@ DEFS := -fno-strict-aliasing \
$(CPPFLAGS) \
$(CFLAGS)
-# set compiler flags for all sanitized builds
-ifdef BOWTIE2_BIN_LIST_SAN
-$(BOWTIE2_BIN_LIST_SAN): CXXFLAGS+=$(SANITIZER_FLAGS)
-else
-$(BOWTIE2_BIN_LIST_SAN): $(error "Compiler does not support...")
-endif
-
#
# bowtie2-build targets
#
-bowtie2-build-s-sanitized bowtie2-build-s: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
+bowtie2-build-s: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
$(CPPFLAGS) \
@@ -313,7 +287,7 @@ bowtie2-build-s-sanitized bowtie2-build-
$(SHARED_CPPS) $(BUILD_CPPS_MAIN) \
$(LDFLAGS) $(LDLIBS)
-bowtie2-build-l-sanitized bowtie2-build-l: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
+bowtie2-build-l: bt2_build.cpp $(SHARED_CPPS) $(HEADERS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
$(CPPFLAGS) \
@@ -341,7 +315,7 @@ bowtie2-build-l-debug: bt2_build.cpp $(S
# bowtie2-align targets
#
-bowtie2-align-s-sanitized bowtie2-align-s: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
+bowtie2-align-s: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
$(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -Wall \
$(CPPFLAGS) \
@@ -349,7 +323,7 @@ bowtie2-align-s-sanitized bowtie2-align-
$(SHARED_CPPS) $(SEARCH_CPPS_MAIN) \
$(LDFLAGS) $(LDLIBS)
-bowtie2-align-l-sanitized bowtie2-align-l: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
+bowtie2-align-l: bt2_search.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(CXXFLAGS) \
$(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) -Wall \
$(CPPFLAGS) \
@@ -379,7 +353,7 @@ bowtie2-align-l-debug: bt2_search.cpp $(
# bowtie2-inspect targets
#
-bowtie2-inspect-s-sanitized bowtie2-inspect-s: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
+bowtie2-inspect-s: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(RELEASE_FLAGS) \
$(RELEASE_DEFS) $(CXXFLAGS) \
$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
@@ -388,7 +362,7 @@ bowtie2-inspect-s-sanitized bowtie2-insp
$(SHARED_CPPS) \
$(LDFLAGS) $(LDLIBS)
-bowtie2-inspect-l-sanitized bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
+bowtie2-inspect-l: bt2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
$(CXX) $(RELEASE_FLAGS) \
$(RELEASE_DEFS) $(CXXFLAGS) \
$(DEFS) -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX -Wall \
@@ -589,7 +563,7 @@ test: simple-test
.PHONY: clean
clean:
- rm -f $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) $(BOWTIE2_BIN_LIST_SAN) \
+ rm -f $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG) \
$(addsuffix .exe,$(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG)) \
bowtie2-*.zip
rm -f core.* .tmp.head
--- a/bowtie2
+++ b/bowtie2
@@ -122,7 +122,6 @@ getBt2Desc(\%desc);
sub isWrapped($) { return defined($wrapped{$_[0]}); }
my $debug = 0;
-my $sanitized = 0;
my %read_fns = ();
my %read_compress = ();
my $cap_out = undef; # Filename for passthrough
@@ -184,7 +183,6 @@ GetOptions(
"keep" => \$keep,
"verbose" => \$verbose,
"debug" => \$debug,
- "sanitized" => \$sanitized,
"large-index" => \$large_idx,
"no-unal" => \$no_unal,
"un=s" => \&handle_un_or_al,
@@ -473,9 +471,6 @@ my $suffix = "";
if ($debug) {
$suffix = "-debug";
}
-elsif($sanitized) {
- $suffix = "-sanitized";
-}
# Construct command invoking bowtie2-align
quote_params(\@bt2_args);
--- a/bowtie2-build
+++ b/bowtie2-build
@@ -46,7 +46,6 @@ def main():
group = parser.add_mutually_exclusive_group()
group.add_argument('--debug', action='store_true')
- group.add_argument('--sanitized', action='store_true')
logging.basicConfig(level=logging.ERROR,
format='%(levelname)s: %(message)s'
@@ -69,9 +68,9 @@ def main():
build_bin_spec += '-debug'
build_bin_l += '-debug'
- if script_options.sanitized:
- build_bin_spec += '-sanitized'
- build_bin_l += '-sanitized'
+# if script_options.sanitized:
+# build_bin_spec += '-sanitized'
+# build_bin_l += '-sanitized'
fastas = []
if '-c' not in argv and len(argv) >= 2:
--- a/bowtie2-inspect
+++ b/bowtie2-inspect
@@ -33,7 +33,6 @@ def main():
group = parser.add_mutually_exclusive_group()
group.add_argument('--debug', action='store_true')
- group.add_argument('--sanitized', action='store_true')
parser.add_argument('--verbose', action='store_true')
parser.add_argument('--large-index', action='store_true')
@@ -60,10 +59,6 @@ def main():
inspect_bin_spec += '-debug'
inspect_bin_l += '-debug'
- if script_options.sanitized:
- inpsect_bin_spec += '-sanitized'
- inspect_bin_l += '-sanitized'
-
if script_options.large_index:
inspect_bin_spec = os.path.join(ex_path,inspect_bin_l)
elif len(argv) >= 1:
--- a/scripts/test/simple_tests.pl
+++ b/scripts/test/simple_tests.pl
@@ -4605,7 +4605,7 @@ sub runbowtie2($$$$$$$$$$$$$$$$$$$$$$$$$
close(FA);
if($do_build) {
my $build_args = "";
- my $cmd = "$bowtie2_build $idx_type --quiet --sanity $build_args $fa .simple_tests.tmp";
+ my $cmd = "$bowtie2_build $idx_type --quiet $build_args $fa .simple_tests.tmp";
print "$cmd\n";
system($cmd);
($? == 0) || die "Bad exitlevel from bowtie2-build: $?";
@@ -4807,7 +4807,7 @@ sub matchSamOptionalFlags($$) {
my $tmpfafn = ".simple_tests.pl.fa";
my $last_ref = undef;
foreach my $large_idx (undef,1) {
- foreach my $binary_type ("release", "debug", "sanitized") {
+ foreach my $binary_type ("release", "debug") {
for (my $ci = 0; $ci < scalar(@cases); $ci++) {
my $c = $cases[$ci];
last unless defined($c);
--- a/scripts/test/simple_tests.sh
+++ b/scripts/test/simple_tests.sh
@@ -21,8 +21,8 @@
# simple_tests.sh
-export ASAN_OPTIONS=halt_on_error=1
-export UBSAN_OPTIONS=halt_on_error=1
+#export ASAN_OPTIONS=halt_on_error=1
+#export UBSAN_OPTIONS=halt_on_error=1
#MAKE=`which gmake || which make`
#$MAKE $* bowtie2-align-s \
--- a/bt2_build.cpp
+++ b/bt2_build.cpp
@@ -147,7 +147,6 @@ static void printUsage(ostream& out) {
out << " --large-index force generated index to be 'large', even if ref" << endl
<< " has fewer than 4 billion nucleotides" << endl
<< " --debug use the debug binary; slower, assertions enabled" << endl
- << " --sanitized use sanitized binary; slower, uses ASan and/or UBSan" << endl
<< " --verbose log the issued command" << endl;
}
out << " -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting" << endl
--- a/bt2_inspect.cpp
+++ b/bt2_inspect.cpp
@@ -81,7 +81,6 @@ static void printUsage(ostream& out) {
out << " --large-index force inspection of the 'large' index, even if a" << endl
<< " 'small' one is present." << endl
<< " --debug use the debug binary; slower, assertions enabled" << endl
- << " --sanitized use sanitized binary; slower, uses ASan and/or UBSan" << endl
<< " --verbose log the issued command" << endl;
}
out << " -a/--across <int> Number of characters across in FASTA output (default: 60)" << endl
|
