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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
spades-3.13.1+dfsg/assembler/ext/include/clipp/clipp.h-6381- os << doc_string(4*level, ' ');
spades-3.13.1+dfsg/assembler/ext/include/clipp/clipp.h:6382: print(os, param.as_param());
spades-3.13.1+dfsg/assembler/ext/include/clipp/clipp.h-6383- }
##############################################
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-71- ++spinCount;
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h:72: asm volatile("pause");
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-73- } else {
##############################################
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-111- bool memVal; // only set if the cmpxchg fails
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h:112: asm volatile("lock; cmpxchgb %[newVal], (%[lockPtr]);"
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-113- "setz %[output];"
##############################################
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-135- while (lock_ != FREE) {
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h:136: asm volatile("" : : : "memory");
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-137- sleeper.wait();
##############################################
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-142- void unlock() {
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h:143: asm volatile("" : : : "memory");
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-144- lock_ = FREE; // release barrier on x86
##############################################
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-220-#define FB_DOBTS(size) \
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h:221: asm volatile("lock; bts" #size " %1, (%2); setnc %0" \
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-222- : "=r" (ret) \
##############################################
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-253-#define FB_DOBTR(size) \
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h:254: asm volatile("lock; btr" #size " %0, (%1)" \
spades-3.13.1+dfsg/assembler/ext/include/folly/SmallLocks.h-255- : \
##############################################
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h-82-
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h:83: asm volatile (
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h-84- "lock; xaddq %0, %1;"
##############################################
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h-96- x = (uint64_t)(-(int64_t)x);
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h:97: asm volatile (
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h-98- "lock; xaddq %0, %1;"
##############################################
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h-194-
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h:195: asm volatile (
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h-196- "lock; xaddl %0, %1;"
##############################################
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h-208- x = (uint32_t)(-(int32_t)x);
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h:209: asm volatile (
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/atomic.h-210- "lock; xaddl %0, %1;"
##############################################
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h-36- /* This is a true memory barrier. */
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h:37: asm volatile ("pusha;"
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h-38- "xor %%eax,%%eax;"
##############################################
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h-49- */
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h:50: asm volatile ("nop;"
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h-51- : /* Outputs. */
##############################################
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h-61-
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h:62: asm volatile ("sfence"
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h-63- : /* Outputs. */
##############################################
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h-72-
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h:73: asm volatile ("eieio"
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h-74- : /* Outputs. */
##############################################
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h-83-
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h:84: asm volatile ("membar #StoreStore"
spades-3.13.1+dfsg/assembler/ext/include/jemalloc/internal/mb.h-85- : /* Outputs. */
##############################################
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h-239-
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h:240: uintptr_t AlignedAddr = alignAddr(NewSlab, Alignment);
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h-241- assert(AlignedAddr + Size <= (uintptr_t)NewSlab + PaddedSize);
##############################################
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h-249- StartNewSlab();
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h:250: uintptr_t AlignedAddr = alignAddr(CurPtr, Alignment);
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h-251- assert(AlignedAddr + Size <= (uintptr_t)End &&
##############################################
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h-381- auto DestroyElements = [](char *Begin, char *End) {
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h:382: assert(Begin == (char*)alignAddr(Begin, alignOf<T>()));
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h-383- for (char *Ptr = Begin; Ptr + sizeof(T) <= End; Ptr += sizeof(T))
##############################################
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h-390- std::distance(Allocator.Slabs.begin(), I));
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h:391: char *Begin = (char*)alignAddr(*I, alignOf<T>());
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h-392- char *End = *I == Allocator.Slabs.back() ? Allocator.CurPtr
##############################################
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h-400- size_t Size = PtrAndSize.second;
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h:401: DestroyElements((char*)alignAddr(Ptr, alignOf<T>()), (char *)Ptr + Size);
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/Allocator.h-402- }
##############################################
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/MathExtras.h-536-/// Alignment should be a power of two. This method rounds up, so
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/MathExtras.h:537:/// alignAddr(7, 4) == 8 and alignAddr(8, 4) == 8.
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/MathExtras.h:538:inline uintptr_t alignAddr(const void *Addr, size_t Alignment) {
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/MathExtras.h-539- assert(Alignment && isPowerOf2_64((uint64_t)Alignment) &&
##############################################
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/MathExtras.h-549-inline size_t alignmentAdjustment(const void *Ptr, size_t Alignment) {
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/MathExtras.h:550: return alignAddr(Ptr, Alignment) - (uintptr_t)Ptr;
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/MathExtras.h-551-}
##############################################
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/TrailingObjects.h-175- return reinterpret_cast<const NextTy *>(
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/TrailingObjects.h:176: llvm::alignAddr(Ptr, alignof(NextTy)));
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/TrailingObjects.h-177- else
##############################################
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/TrailingObjects.h-189- if (requiresRealignment())
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/TrailingObjects.h:190: return reinterpret_cast<NextTy *>(llvm::alignAddr(Ptr, alignof(NextTy)));
spades-3.13.1+dfsg/assembler/ext/include/llvm/Support/TrailingObjects.h-191- else
##############################################
spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c-167- struct in_addr addr;
spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:168: addr.s_addr = inet_addr(host);
spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:169: hp = gethostbyaddr((char*)&addr, 4, AF_INET);
spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c-170- }
##############################################
spades-3.13.1+dfsg/assembler/ext/src/llvm/Path.inc-155- Dl_info DLInfo;
spades-3.13.1+dfsg/assembler/ext/src/llvm/Path.inc:156: int err = dladdr(MainAddr, &DLInfo);
spades-3.13.1+dfsg/assembler/ext/src/llvm/Path.inc-157- if (err == 0)
##############################################
spades-3.13.1+dfsg/assembler/ext/src/llvm/Signals.inc-320- Dl_info dlinfo;
spades-3.13.1+dfsg/assembler/ext/src/llvm/Signals.inc:321: dladdr(StackTrace[i], &dlinfo);
spades-3.13.1+dfsg/assembler/ext/src/llvm/Signals.inc-322- const char* name = strrchr(dlinfo.dli_fname, '/');
##############################################
spades-3.13.1+dfsg/assembler/ext/src/llvm/Signals.inc-332- Dl_info dlinfo;
spades-3.13.1+dfsg/assembler/ext/src/llvm/Signals.inc:333: dladdr(StackTrace[i], &dlinfo);
spades-3.13.1+dfsg/assembler/ext/src/llvm/Signals.inc-334-
##############################################
spades-3.13.1+dfsg/assembler/ext/src/samtools/Makefile-26-all-recur lib-recur clean-recur cleanlocal-recur install-recur:
spades-3.13.1+dfsg/assembler/ext/src/samtools/Makefile:27: @target=`echo $@ | sed s/-recur//`; \
spades-3.13.1+dfsg/assembler/ext/src/samtools/Makefile-28- wdir=`pwd`; \
##############################################
spades-3.13.1+dfsg/assembler/ext/src/samtools/bcftools/Makefile-16-all-recur lib-recur clean-recur cleanlocal-recur install-recur:
spades-3.13.1+dfsg/assembler/ext/src/samtools/bcftools/Makefile:17: @target=`echo $@ | sed s/-recur//`; \
spades-3.13.1+dfsg/assembler/ext/src/samtools/bcftools/Makefile-18- wdir=`pwd`; \
##############################################
spades-3.13.1+dfsg/assembler/ext/src/samtools/knetfile.c-167- struct in_addr addr;
spades-3.13.1+dfsg/assembler/ext/src/samtools/knetfile.c:168: addr.s_addr = inet_addr(host);
spades-3.13.1+dfsg/assembler/ext/src/samtools/knetfile.c:169: hp = gethostbyaddr((char*)&addr, 4, AF_INET);
spades-3.13.1+dfsg/assembler/ext/src/samtools/knetfile.c-170- }
##############################################
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/Makefile-18-lib-recur all-recur clean-recur cleanlocal-recur install-recur:
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/Makefile:19: @target=`echo $@ | sed s/-recur//`; \
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/Makefile-20- wdir=`pwd`; \
##############################################
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck-61- if ( !exists($$opts{prefix}) ) { error("Expected -p parameter.\n") }
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck:62: if ( $$opts{prefix}=~m{/$} ) { `mkdir -p $$opts{prefix}`; }
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck-63- elsif ( !($$opts{prefix}=~/-$/) ) { $$opts{prefix} .= '-'; }
##############################################
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck-150- my $cmd = "gnuplot $cmdfile";
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck:151: system($cmd);
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck-152- if ( $? ) { error("The command exited with non-zero status $?:\n\t$cmd\n\n"); }
##############################################
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck-216- $dir =~ s{/[^/]+$}{};
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck:217: if ( $dir && $dir ne $gp_file ) { `mkdir -p $dir`; }
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck-218-
##############################################
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck-833- {
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck:834: my (@lines) = `cat $$opts{bamcheck} | grep ^$tag | wc -l`;
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck-835- chomp($lines[0]);
##############################################
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck-845- my $args = get_defaults($opts,"$$opts{prefix}mism-per-cycle.png");
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck:846: my ($nquals) = `grep ^MPC $$opts{bamcheck} | awk '\$2==1' | sed 's,\\t,\\n,g' | wc -l`;
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck:847: my ($ncycles) = `grep ^MPC $$opts{bamcheck} | wc -l`;
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/plot-bamcheck-848- chomp($nquals);
##############################################
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/sam2vcf.pl-237- my $cmd = "samtools faidx $$self{file} $chr:$pos-$to";
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/sam2vcf.pl:238: my @out = `$cmd`;
spades-3.13.1+dfsg/assembler/ext/src/samtools/misc/sam2vcf.pl-239- if ( $? ) { $self->throw("$cmd: $!"); }
##############################################
spades-3.13.1+dfsg/assembler/src/cmake/Modules/GetGitRevisionDescription.cmake-76- @ONLY)
spades-3.13.1+dfsg/assembler/src/cmake/Modules/GetGitRevisionDescription.cmake:77: include("${GIT_DATA}/grabRef.cmake")
spades-3.13.1+dfsg/assembler/src/cmake/Modules/GetGitRevisionDescription.cmake-78-
##############################################
spades-3.13.1+dfsg/assembler/src/common/sequence/levenshtein.hpp-84- // Berghel, Hal ; Roach, David : "An Extension of Ukkonen's
spades-3.13.1+dfsg/assembler/src/common/sequence/levenshtein.hpp:85: // Enhanced Dynamic Programming ASM Algorithm"
spades-3.13.1+dfsg/assembler/src/common/sequence/levenshtein.hpp-86- // (http://www.acm.org/~hlb/publications/asm/asm.html)
##############################################
spades-3.13.1+dfsg/assembler/src/common/sequence/levenshtein.hpp-172- // Berghel, Hal ; Roach, David : "An Extension of Ukkonen's
spades-3.13.1+dfsg/assembler/src/common/sequence/levenshtein.hpp:173: // Enhanced Dynamic Programming ASM Algorithm"
spades-3.13.1+dfsg/assembler/src/common/sequence/levenshtein.hpp-174- // (http://www.acm.org/~hlb/publications/asm/asm.html)
##############################################
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-32- unless (fork) {
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:33: my_exec("cat $input_folder/$num.reads.left.corrected $input_folder/$num.reads.right.corrected > $input_folder/$num.reads.all.corrected");
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-34- die("$num reads concatenated.");
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-35- }
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:36: my_exec("mkdir $dir/tmpdir$num");
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-37- chdir "$dir/tmpdir$num";
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:38: my_exec("$count_command $input_folder/$num.kmers.solid $input_folder/$num.countkmers.solid 2 500");
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:39: my_exec($cleanup_command);
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:40: my_exec("$count_command $input_folder/$num.kmers.bad $input_folder/$num.countkmers.bad 2 500");
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:41: my_exec($cleanup_command);
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-42- wait(); # cat and previous iteration processes have finished
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:43: my_exec("$count_command $input_folder/$num.reads.all.corrected $input_folder/$num.countkmers.reads 2 500");
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:44: my_exec($cleanup_command);
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-45- chdir "$dir";
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:46: my_exec("rm -rf tmpdir$num");
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-47- # correction can be done in parallel -- it doesn't open 500 files at once
##############################################
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-49- unless (fork) {
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:50: my_exec("$correct_command $biggenome $input_folder/$num.countkmers.solid $input_folder/$num.countkmers.bad > $output_folder/$num.results.solidkmers");
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-51- die("$num solid kmer quality estimated by process $$.");
##############################################
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-53- unless (fork) {
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl:54: my_exec("/home/snikolenko/algorithmic-biology/assembler/build/release/hammer/quake_enhanced/test_correction_quality/test_correction_quality $biggenome $input_folder/$num.countkmers.reads $input_folder/$num.countkmers.bad > $output_folder/$num.results.newreads");
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/getresults.pl-55- die("$num reads quality estimated by process $$.");
##############################################
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/memusg-13-
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/memusg:14:pgid=`ps -o pgid= $$`
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/memusg-15-# make sure we're in a separate process group
##############################################
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/memusg-32-peak=0
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/memusg:33:while sizes=`sizes $pgid`
spades-3.13.1+dfsg/assembler/src/projects/hammer/misc/memusg-34-do
##############################################
spades-3.13.1+dfsg/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh-18-
spades-3.13.1+dfsg/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh:19:tempfile=`basename $1`.tmp
spades-3.13.1+dfsg/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh:20:indxfile=`basename $1`
spades-3.13.1+dfsg/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh-21-
##############################################
spades-3.13.1+dfsg/assembler/src/tools/contig_analysis/visualizer/misassemblies.py-325- total = 0
spades-3.13.1+dfsg/assembler/src/tools/contig_analysis/visualizer/misassemblies.py:326: sim_block_ids_within_asm = [-1 for jj in range(0, len(self.assemblies))]
spades-3.13.1+dfsg/assembler/src/tools/contig_analysis/visualizer/misassemblies.py-327- sim_block_ids_within_asm[i] = block_num
##############################################
spades-3.13.1+dfsg/assembler/src/tools/contig_analysis/visualizer/misassemblies.py-362- max_pos = 0
spades-3.13.1+dfsg/assembler/src/tools/contig_analysis/visualizer/misassemblies.py:363: for asm in self.assemblies:
spades-3.13.1+dfsg/assembler/src/tools/contig_analysis/visualizer/misassemblies.py-364- asm_max_pos = asm.blocks[len(asm.blocks) - 1].end
##############################################
spades-3.13.1+dfsg/assembler/src/tools/de_quality/alignment/align.sh-16- echo "$LINE1 $LINE2";
spades-3.13.1+dfsg/assembler/src/tools/de_quality/alignment/align.sh:17: echo `grep -A1 $LINE2 distance_estimation.sqn` > "$LINE1""_""$LINE2.fasta"
spades-3.13.1+dfsg/assembler/src/tools/de_quality/alignment/align.sh:18: echo `grep -A1 $LINE1 distance_estimation.sqn` >> "$LINE1""_""$LINE2.fasta"
spades-3.13.1+dfsg/assembler/src/tools/de_quality/alignment/align.sh-19- sed -i 's/\s/\n/' "$LINE1""_""$LINE2.fasta"
##############################################
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh-14- i=$3
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh:15: i=`expr $i - 1`
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh-16-fi
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh:17:STRR=`wc -l $1`
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh:18:SIZZE=`echo $STRR | cut --delimiter=' ' -f 1`
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh-19-PROJ_DIR=`pwd`;
##############################################
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh-23-while [ $i -lt $SIZZE ]; do
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh:24: i=`expr $i + 1`;
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh-25- echo "Iteration "$i" of "$SIZZE
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh:26: LINE=`head -$i $1 | tail -1`
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh-27- LINE1=$(echo "$LINE" | sed 's/\([0-9]*\).*/\1/' );
##############################################
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh-29- echo "$LINE1 $LINE2";
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh:30: f=`find $OUTPUT_DIR/hists/ -name $LINE1"_"$LINE2*`
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh-31- echo "Dir "$f
##############################################
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh-38- gnuplot png_plot.conf > /dev/null 2> /dev/null || { echo "Gnuplot exited "; exit 1; }
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh:39: name=`basename $f`
spades-3.13.1+dfsg/assembler/src/tools/de_quality/genPics.sh-40- cd $OUTPUT_DIR
##############################################
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh-16-fi
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh:17:STRR=`wc -l $1`
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh:18:SIZZE=`echo $STRR | cut --delimiter=' ' -f 1`
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh-19-PROJ_DIR=`pwd`;
##############################################
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh-23-while [ $i -lt $SIZZE ]; do
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh:24: i=`expr $i + 1`;
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh-25- echo "Iteration "$i" of "$SIZZE
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh:26: LINE=`head -$i $1 | tail -1`
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh-27- LINE1=$(echo "$LINE" | sed 's/\([0-9]*\).*/\1/' );
##############################################
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh-29- echo "$LINE1 $LINE2";
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh:30: f=`find $OUTPUT_DIR/hists/ -name $LINE1"_"$LINE2*`
spades-3.13.1+dfsg/assembler/src/tools/de_quality/lookAtPics.sh-31- echo "Dir "$f
##############################################
spades-3.13.1+dfsg/assembler/src/tools/estimation_deprecated/assemblathon/assess_assembly.pl-63-print "\tChecing nucmer file...\n";
spades-3.13.1+dfsg/assembler/src/tools/estimation_deprecated/assemblathon/assess_assembly.pl:64:if (`tail -n 1 ${header}.coords | awk '{print NF}'` < 13) {die "Nucmer ended early.\n"}
spades-3.13.1+dfsg/assembler/src/tools/estimation_deprecated/assemblathon/assess_assembly.pl-65-print "\t...nucmer complete.\n";
##############################################
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/drawplot.pl-51- my $lines = "$begin,$end" . "p";
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/drawplot.pl:52: my $plot = `sed -n '$lines' $prefix.$k.tex`;
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/drawplot.pl-53- print "\%$prefix k=$k:\n";
##############################################
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/runjelly.pl-33-for (my $k = $min_k; $k <= $max_k; $k += 2) {
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/runjelly.pl:34: my_exec("mkdir $pref/$k");
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/runjelly.pl:35: my_exec( "jellyfish count --both-strands -m $k -o $pref/$k/jh -c $indbytes -s $mem -t $numthreads $inp" );
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/runjelly.pl:36: my_exec( "jellyfish dump -c -t -o $pref/$k/dump.tsv $pref/$k/jh_0" );
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/runjelly.pl-37- print " === k-mer statistics for k=$k ===\n";
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/runjelly.pl:38: my_exec( "jellyfish stats $pref/$k/jh_0" );
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/runjelly.pl-39- print " === k-mer statistics for k=$k ===\n";
##############################################
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/runqcount.pl-34-for (my $k = $min_k; $k <= $max_k; $k += 2) {
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/runqcount.pl:35: my_exec( "jellyfish count --both-strands -m $k -o $pref$k -c $indbytes -s $mem -t $numthreads $inp" );
spades-3.13.1+dfsg/assembler/src/tools/kmersongenome/runqcount.pl-36-}
##############################################
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/CABOG_assemble.sh-11-RUNNER_PARAM_CABOG_BASE/fastqToCA -insertsize RUNNER_PARAM_INSERT_SIZE RUNNER_PARAM_DEVIATION -type 'RUNNER_PARAM_PHRED_TYPE' -libraryname reads -mates RUNNER_PARAM_LEFT,RUNNER_PARAM_RIGHT >reads.frg 2>>RUNNER_PARAM_STDERR_LOG
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/CABOG_assemble.sh:12:RUNNER_PARAM_CABOG_BASE/runCA -d . -p asm -s RUNNER_PARAM_CABOG_CONFIG reads.frg >> RUNNER_PARAM_STDOUT_LOG 2>> RUNNER_PARAM_STDERR_LOG
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/CABOG_assemble.sh-13-
##############################################
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/CABOG_mp_assemble.sh-12-RUNNER_PARAM_CABOG_BASE/fastqToCA -insertsize RUNNER_PARAM_MP_INSERT_SIZE RUNNER_PARAM_MP_DEVIATION -type 'RUNNER_PARAM_PHRED_TYPE' RUNNER_PARAM_MP_ORIENT -libraryname mp_reads -mates RUNNER_PARAM_MP_LEFT,RUNNER_PARAM_MP_RIGHT >mp_reads.frg 2>>RUNNER_PARAM_STDERR_LOG
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/CABOG_mp_assemble.sh:13:RUNNER_PARAM_CABOG_BASE/runCA -d . -p asm -s RUNNER_PARAM_CABOG_CONFIG reads.frg mp_reads.frg >> RUNNER_PARAM_STDOUT_LOG 2>> RUNNER_PARAM_STDERR_LOG
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/CABOG_mp_assemble.sh-14-
##############################################
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/SOAP_assemble.sh-10-
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/SOAP_assemble.sh:11:RUNNER_PARAM_SOAP_BASE/SOAPdenovo-127mer all -K RUNNER_PARAM_K -F -R -E -w -u -s RUNNER_PARAM_SOAP_CONFIG -o asm -p RUNNER_PARAM_THREADS
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/SOAP_assemble.sh-12-RUNNER_PARAM_SOAP_BASE/GapCloser -b RUNNER_PARAM_SOAP_CONFIG -a asm.scafSeq -o asm.new.scafSeq -t RUNNER_PARAM_THREADS
##############################################
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/runner.py-249- log_file = open(log_filename, 'a')
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/runner.py:250: cmd_line = os.path.join(abyss_base, "abyss-pe") + " k=%d n=5 s=100 name=asm lib='reads' reads='%s %s'" % \
spades-3.13.1+dfsg/assembler/src/tools/misc/assembler_runner/runner.py-251- (K, left, right) + " -j " + str(max_threads)
##############################################
spades-3.13.1+dfsg/assembler/src/tools/res_counter/measure_all.sh-29-# converting to absolute paths
spades-3.13.1+dfsg/assembler/src/tools/res_counter/measure_all.sh:30:output_base=`readlink -e $output_base`
spades-3.13.1+dfsg/assembler/src/tools/res_counter/measure_all.sh:31:res_counter=`readlink -e $res_counter`
spades-3.13.1+dfsg/assembler/src/tools/res_counter/measure_all.sh:32:res_saver=`readlink -e $res_saver`
spades-3.13.1+dfsg/assembler/src/tools/res_counter/measure_all.sh-33-
##############################################
spades-3.13.1+dfsg/assembler/src/tools/res_counter/spades_pipeline_measurer.sh-51-rm maxmem.txt
spades-3.13.1+dfsg/assembler/src/tools/res_counter/spades_pipeline_measurer.sh:52:previous_stage_size=`du -hs $spades_output_dir | cut -f1`
spades-3.13.1+dfsg/assembler/src/tools/res_counter/spades_pipeline_measurer.sh-53-
##############################################
spades-3.13.1+dfsg/assembler/src/tools/res_counter/spades_pipeline_measurer.sh-64-rm maxmem.txt
spades-3.13.1+dfsg/assembler/src/tools/res_counter/spades_pipeline_measurer.sh:65:previous_stage_size=`du -hs $spades_output_dir | cut -f1`
spades-3.13.1+dfsg/assembler/src/tools/res_counter/spades_pipeline_measurer.sh-66-
##############################################
spades-3.13.1+dfsg/assembler/src/tools/res_counter/run.pl-8-
spades-3.13.1+dfsg/assembler/src/tools/res_counter/run.pl:9:system("gcc $script_dir/pstree.c -o $script_dir/pstree");
spades-3.13.1+dfsg/assembler/src/tools/res_counter/run.pl-10-
##############################################
spades-3.13.1+dfsg/assembler/src/tools/spades_build/tag-bug-fix.sh-26-then
spades-3.13.1+dfsg/assembler/src/tools/spades_build/tag-bug-fix.sh:27: FIX=`cat $FILE`
spades-3.13.1+dfsg/assembler/src/tools/spades_build/tag-bug-fix.sh-28-else
##############################################
spades-3.13.1+dfsg/assembler/spades_compile.sh-15-BUILD_DIR=build_spades
spades-3.13.1+dfsg/assembler/spades_compile.sh:16:BASEDIR=`pwd`/`dirname $0`
spades-3.13.1+dfsg/assembler/spades_compile.sh-17-
##############################################
spades-3.13.1+dfsg/debian/bin/spades-3-SPADESSHARE=/usr/share/spades
spades-3.13.1+dfsg/debian/bin/spades:4:exename=`basename $0`
spades-3.13.1+dfsg/debian/bin/spades-5-PATH=$SPADESDIR:$PATH
##############################################
spades-3.13.1+dfsg/debian/createmanpages-1-#!/bin/sh
spades-3.13.1+dfsg/debian/createmanpages:2:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//'`
spades-3.13.1+dfsg/debian/createmanpages-3-MANDIR=debian/mans
##############################################
spades-3.13.1+dfsg/.pc/0110_build_single_thread.patch/assembler/spades_compile.sh-15-BUILD_DIR=build_spades
spades-3.13.1+dfsg/.pc/0110_build_single_thread.patch/assembler/spades_compile.sh:16:BASEDIR=`pwd`/`dirname $0`
spades-3.13.1+dfsg/.pc/0110_build_single_thread.patch/assembler/spades_compile.sh-17-
##############################################
spades-3.13.1+dfsg/.pc/0115_enable_compiler_messages.patch/assembler/spades_compile.sh-15-BUILD_DIR=build_spades
spades-3.13.1+dfsg/.pc/0115_enable_compiler_messages.patch/assembler/spades_compile.sh:16:BASEDIR=`pwd`/`dirname $0`
spades-3.13.1+dfsg/.pc/0115_enable_compiler_messages.patch/assembler/spades_compile.sh-17-
##############################################
spades-3.13.1+dfsg/.pc/0117_build_with_debug.patch/assembler/spades_compile.sh-15-BUILD_DIR=build_spades
spades-3.13.1+dfsg/.pc/0117_build_with_debug.patch/assembler/spades_compile.sh:16:BASEDIR=`pwd`/`dirname $0`
spades-3.13.1+dfsg/.pc/0117_build_with_debug.patch/assembler/spades_compile.sh-17-
##############################################
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/misc/assembler_runner/runner.py-249- log_file = open(log_filename, 'a')
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/misc/assembler_runner/runner.py:250: cmd_line = os.path.join(abyss_base, "abyss-pe") + " k=%d n=5 s=100 name=asm lib='reads' reads='%s %s'" % \
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/misc/assembler_runner/runner.py-251- (K, left, right) + " -j " + str(max_threads)
##############################################
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/contig_analysis/visualizer/misassemblies.py-325- total = 0
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/contig_analysis/visualizer/misassemblies.py:326: sim_block_ids_within_asm = [-1 for jj in range(0, len(self.assemblies))]
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/contig_analysis/visualizer/misassemblies.py-327- sim_block_ids_within_asm[i] = block_num
##############################################
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/contig_analysis/visualizer/misassemblies.py-362- max_pos = 0
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/contig_analysis/visualizer/misassemblies.py:363: for asm in self.assemblies:
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/contig_analysis/visualizer/misassemblies.py-364- asm_max_pos = asm.blocks[len(asm.blocks) - 1].end
##############################################
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh-18-
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh:19:tempfile=`basename $1`.tmp
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh:20:indxfile=`basename $1`
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh-21-
##############################################
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/res_counter/run.pl-8-
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/res_counter/run.pl:9:system("gcc $script_dir/pstree.c -o $script_dir/pstree");
spades-3.13.1+dfsg/.pc/python3.patch/assembler/src/tools/res_counter/run.pl-10-