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Functions40,422 in github.com/ablab/spades

↓ 24 callersFunctionresetUpper
Storage order of the matrix
ext/include/blaze/blaze/math/expressions/DenseMatrix.h:516
↓ 24 callersMethodrows
Rows function !\brief Returns the current number of rows of the matrix. // // \return The number of rows of the matrix. */
ext/include/blaze/blaze/math/expressions/DMatTransExpr.h:263
↓ 24 callersMethodrows
Compile time column arguments
ext/include/blaze/blaze/math/views/columns/Sparse.h:1040
↓ 24 callersMethodsize
Size function !\brief Returns the current size/dimension of the vector. // // \return The size of the vector. */
ext/include/blaze/blaze/math/expressions/DVecNoAliasExpr.h:241
↓ 24 callersMethodsize
Size function !\brief Returns the current size/dimension of the vector. // // \return The size of the vector. */
ext/include/blaze/blaze/math/expressions/DVecNoSIMDExpr.h:223
↓ 24 callersFunctiontrmv
Storage order of the matrix operand
ext/include/blaze/blaze/math/blas/trmv.h:104
↓ 24 callersFunctiontrySet
Type of the element
ext/include/blaze/blaze/math/views/Row.h:1272
↓ 24 callersMethodvalue
Value function !\brief Access to the current value of the sparse row element. // // \return The current value of the sparse row element.
ext/include/blaze/blaze/math/views/rows/Sparse.h:2388
↓ 24 callersMethodvalue
Value function !\brief Access to the current value of the sparse column element. // // \return The current value of the sparse column elem
ext/include/blaze/blaze/math/views/columns/Sparse.h:2380
↓ 24 callersMethodwhat
ext/src/bamtools/api/internal/utils/BamException_p.h:39
↓ 24 callersMethodwrite_indent
(self)
ext/src/python_libs/pyyaml3/emitter.py:813
↓ 23 callersFunctionContainerEq
ext/src/googletest/googlemock/include/gmock/gmock-matchers.h:4970
↓ 23 callersMethodDetach
src/common/assembly_graph/core/action_handlers.hpp:139
↓ 23 callersFunctionH2
ext/include/parallel_hashmap/phmap.h:360
↓ 23 callersFunctionIsPrime
Returns true if and only if n is a prime number.
ext/src/googletest/googletest/samples/sample1.cc:45
↓ 23 callersFunctionIsValidEscape
Returns true if and only if "\\c" is a supported escape sequence.
ext/src/googletest/googletest/src/gtest-port.cc:775
↓ 23 callersMethodMapSequence
src/common/alignment/kmer_sequence_mapper.cpp:25
↓ 23 callersFunctionStartsWith
ext/src/googletest/googlemock/include/gmock/gmock-matchers.h:4781
↓ 23 callersFunction_mm_set1_epi32
Sets the 4 signed 32-bit integer values to i. r0 := i r1 := i r2 := i r3 := I https://msdn.microsoft.com/en-us/library/vstudio/h4xscxat(v=vs.100).as
ext/include/sse2neon/sse2neon.h:5197
↓ 23 callersMethodattribute
Emit an attribute whose value is self-contained (number, vector<int> etc).
ext/include/llvm/Support/JSON.h:799
↓ 23 callersFunctionbam_aux_get
ext/src/samtools/bam_aux.c:36
↓ 23 callersFunctionbam_header_destroy
ext/src/samtools/bam.c:63
↓ 23 callersMethodbegin
ext/include/parallel_hashmap/phmap.h:265
↓ 23 callersMethodbegin
ext/include/boost/property_tree/detail/ptree_implementation.hpp:242
↓ 23 callersMethodbegin
Compile time subvector arguments
ext/include/blaze/blaze/math/views/subvector/Dense.h:1001
↓ 23 callersFunctionbeta
ext/include/boost/math/special_functions/beta.hpp:1564
↓ 23 callersMethodbump
ext/src/lexy/include/lexy/input/base.hpp:44
↓ 23 callersMethodcolumns
Columns function !\brief Returns the current number of columns of the matrix. // // \return The number of columns of the matrix. */
ext/include/blaze/blaze/math/expressions/DMatScalarDivExpr.h:542
↓ 23 callersMethodcolumns
Columns function !\brief Returns the current number of columns of the matrix. // // \return The number of columns of the matrix. */
ext/include/blaze/blaze/math/expressions/DMatScalarMultExpr.h:538
↓ 23 callersMethodcolumns
Columns function !\brief Returns the current number of columns of the matrix. // // \return The number of columns of the matrix. */
ext/include/blaze/blaze/math/expressions/SMatTransExpr.h:233
↓ 23 callersMethodend
src/projects/binspreader/id_map.hpp:126
↓ 23 callersFunctionesl_mem_strtoi
Function: esl_mem_strtoi() * Synopsis: Convert a chunk of memory to an int. * Incept: SRE, Thu 02 Aug 2018 [Slaid Cleaves, Junkyard] * * Purp
ext/src/easel/esl_mem.c:233
↓ 23 callersFunctionesl_stack_IPop
Function: esl_stack_IPop() * Synopsis: Pop an integer off a stack. * Incept: SRE, Sun Dec 26 09:19:12 2004 [Zaragoza] * * Purpose: Pops an
ext/src/easel/esl_stack.c:330
↓ 23 callersFunctionesl_vec_FCopy
ext/src/easel/esl_vectorops.c:494
↓ 23 callersMethodexpansion
! \cond BLAZE_INTERNAL */ !\brief Returns the expansion of the expansion expression. // // \return The expansion. */
ext/include/blaze/blaze/math/expressions/ExpandExprData.h:150
↓ 23 callersMethodflags
src/common/hmm/hmmmatcher.cpp:226
↓ 23 callersMethodgetCategory
ext/src/llvm/APFloat.cpp:4502
↓ 23 callersFunctionget_slot
ext/src/gqf/gqf.c:331
↓ 23 callersFunctionif
ext/include/boost/math/special_functions/gamma.hpp:1531
↓ 23 callersMethodindex
Index function !\brief Access to the current index of the sparse element. // // \return The current index of the sparse element. */
ext/include/blaze/blaze/math/views/rows/Sparse.h:2398
↓ 23 callersMethodindex
Index function !\brief Access to the current index of the sparse element. // // \return The current index of the sparse element. */
ext/include/blaze/blaze/math/views/columns/Sparse.h:2390
↓ 23 callersFunctionisHermitian
Storage order
ext/include/blaze/blaze/math/Matrix.h:186
↓ 23 callersMethodis_empty
GraphCursor() = default;
src/projects/pathracer/graph.hpp:44
↓ 23 callersMethodkmer
src/projects/hammer/kmer_data.hpp:59
↓ 23 callersMethodlog
(self, s)
src/test/teamcity/teamcity_workflow/workflow_base.py:24
↓ 23 callersFunctionmake_iterator
ext/include/boost/multi_index/sequenced_index.hpp:711
↓ 23 callersFunctionmap
Type of the custom operation
ext/include/blaze/blaze/math/expressions/DMatDMatMapExpr.h:1143
↓ 23 callersFunctionmi_page_block_size
Get the block size of a page (special case for huge objects)
ext/src/mimalloc/include/mimalloc-internal.h:486
↓ 23 callersFunctionmi_page_heap
Heap access
ext/src/mimalloc/include/mimalloc-internal.h:524
↓ 23 callersFunctionp7_oprofile_Create
Function: p7_oprofile_Create() * Synopsis: Allocate an optimized profile structure. * Incept: SRE, Sun Nov 25 12:03:19 2007 [Casa de Gatos] *
ext/src/hmmer/src/impl_sse/p7_oprofile.c:48
↓ 23 callersFunctionp7_pli_NewModel
Function: p7_pli_NewModel() * Synopsis: Prepare pipeline for a new model (target or query) * * Purpose: Caller has a new model <om>. Prepare th
ext/src/hmmer/src/p7_pipeline.c:491
↓ 23 callersFunctionparse
(handler, file_type)
src/projects/spades/pipeline/spades_pipeline/common/SeqIO.py:100
↓ 23 callersMethodprecision
ext/include/cppformat/format.h:1031
↓ 23 callersFunctionpush_back_all
src/common/utils/stl_utils.hpp:41
↓ 23 callersMethodread
src/common/hmm/hmmfile.cpp:111
↓ 23 callersMethodrows
Rows function !\brief Returns the current number of rows of the matrix. // // \return The number of rows of the matrix. */
ext/include/blaze/blaze/math/expressions/DMatScalarDivExpr.h:532
↓ 23 callersMethodrows
Rows function !\brief Returns the current number of rows of the matrix. // // \return The number of rows of the matrix. */
ext/include/blaze/blaze/math/expressions/DMatScalarMultExpr.h:528
↓ 23 callersMethodrows
Rows function !\brief Returns the current number of rows of the matrix. // // \return The number of rows of the matrix. */
ext/include/blaze/blaze/math/expressions/SMatTransExpr.h:223
↓ 22 callersFunctionGetInt
src/projects/online_vis/vis_utils.hpp:25
↓ 22 callersMethodIncomingEdges
src/common/assembly_graph/core/graph_core.hpp:625
↓ 22 callersMethodIsEnd
src/common/adt/queue_iterator.hpp:488
↓ 22 callersFunctionIsNull
ext/src/googletest/googletest/test/gtest-unittest-api_test.cc:132
↓ 22 callersFunctionPointwise
ext/src/googletest/googlemock/include/gmock/gmock-matchers.h:5002
↓ 22 callersFunction_mm_adds_epi16
Adds the 8 signed 16-bit integers in a to the 8 signed 16-bit integers in b and saturates. r0 := SignedSaturate(a0 + b0) r1 := SignedSaturate(a1 + b1
ext/include/sse2neon/sse2neon.h:3053
↓ 22 callersFunction_mm_max_ps
Computes the maximums of the four single-precision, floating-point values of a and b. https://msdn.microsoft.com/en-us/library/vstudio/ff5d607a(v=vs.1
ext/include/sse2neon/sse2neon.h:2010
↓ 22 callersFunction_mm_move_sd
Move the lower double-precision (64-bit) floating-point element from b to the lower element of dst, and copy the upper element from a to the upper ele
ext/include/sse2neon/sse2neon.h:4750
↓ 22 callersFunction_mmxxx_or_si
ext/src/spoa/src/simd_alignment_engine_implementation.hpp:76
↓ 22 callersFunctionany_of
ext/include/llvm/ADT/STLExtras.h:1480
↓ 22 callersMethodbegin
src/common/auxiliary_graphs/contracted_graph/contracted_graph.hpp:33
↓ 22 callersMethodbegin
Storage order of the adapted dense matrix
ext/include/blaze/blaze/math/adaptors/lowermatrix/Dense.h:1372
↓ 22 callersFunctionclear
Type tag
ext/include/blaze/blaze/math/dense/StaticMatrix.h:6945
↓ 22 callersMethodclear
src/projects/spades/hybrid_gap_closer.hpp:264
↓ 22 callersMethodcolumn
! \cond BLAZE_INTERNAL */ !\brief Returns the index of the first column of the submatrix in the underlying matrix. // // \return The index of the firs
ext/include/blaze/blaze/math/views/submatrix/SubmatrixData.h:191
↓ 22 callersMethodend
ext/include/llvm/ADT/STLExtras.h:723
↓ 22 callersMethodend
ext/include/boost/algorithm/string/detail/util.hpp:50
↓ 22 callersMethodend
Compile time row arguments
ext/include/blaze/blaze/math/views/row/Dense.h:655
↓ 22 callersFunctionenumerate
ext/include/llvm/ADT/STLExtras.h:1868
↓ 22 callersFunctionesl_buffer_SetAnchor
Function: esl_buffer_SetAnchor() * Synopsis: Sets an anchor in an input stream. * * Purpose: Set an anchor at byte <offset> (in input coords) i
ext/src/easel/esl_buffer.c:720
↓ 22 callersFunctionesl_keyhash_Destroy
Function: esl_keyhash_Destroy() * Synopsis: Frees a keyhash. * * Purpose: Destroys <kh>. * * Returns: (void) */
ext/src/easel/esl_keyhash.c:186
↓ 22 callersFunctionesl_recorder_Read
Function: esl_recorder_Read() * Synopsis: Read next line of a stream through an <ESL_RECORDER>. * Incept: SRE, Fri Dec 25 16:31:00 2009 [Casa d
ext/src/easel/esl_recorder.c:284
↓ 22 callersMethodgood
src/projects/hammer/kmer_stat.hpp:141
↓ 22 callersMethodname
src/common/alignment/sequence_mapper_notifier.hpp:53
↓ 22 callersMethodnext
src/common/io/sra/sra_parser.cpp:29
↓ 22 callersFunctionoperator
ext/src/mimalloc/src/alloc-override.c:165
↓ 22 callersFunctionp7_alidisplay_Destroy
Function: p7_alidisplay_Destroy() * Synopsis: Frees a <P7_ALIDISPLAY> */
ext/src/hmmer/src/p7_alidisplay.c:1021
↓ 22 callersFunctionp7_pli_NewSeq
Function: p7_pli_NewSeq() * Synopsis: Prepare pipeline for a new sequence (target or query) * * Purpose: Caller has a new sequence <sq>. Prepar
ext/src/hmmer/src/p7_pipeline.c:575
↓ 22 callersFunctionp7_trace_CreateWithPP
Function: p7_trace_CreateWithPP() * Synopsis: Allocates a traceback that includes posterior probs. * Incept: SRE, Tue Aug 19 13:08:12 2008 [Jan
ext/src/hmmer/src/p7_trace.c:65
↓ 22 callersMethodrow
! \cond BLAZE_INTERNAL */ !\brief Returns the index of the first row of the submatrix in the underlying matrix. // // \return The index of the first r
ext/include/blaze/blaze/math/views/submatrix/SubmatrixData.h:177
↓ 22 callersMethodsize
src/common/sequence/sequence.hpp:631
↓ 22 callersMethodsize
src/common/auxiliary_graphs/contracted_graph/contracted_graph.hpp:31
↓ 22 callersMethodsize
ext/include/boomphf/BooPHF.h:489
↓ 22 callersMethodsize
Size function !\brief Returns the current size/dimension of the vector. // // \return The size of the vector. */
ext/include/blaze/blaze/math/expressions/SVecTransExpr.h:214
↓ 22 callersMethodsize
Size function !\brief Returns the current size/dimension of the vector. // // \return The size of the vector. */
ext/include/blaze/blaze/math/expressions/SVecMapExpr.h:358
↓ 22 callersFunctionsrand
ext/include/nlopt/nlopt.hpp:568
↓ 22 callersMethodstr
src/projects/corrector/positional_read.cpp:16
↓ 22 callersMethodstr
ext/include/clipp/clipp.h:6110
↓ 22 callersFunctionswap
Density flag
ext/include/blaze/blaze/math/adaptors/LowerMatrix.h:286
↓ 22 callersMethodtop
ext/include/radix_heap/radix_heap.h:129
↓ 22 callersFunctiontry
do a raw inflate of data in hexadecimal with both inflate and inflateBack */
ext/src/zlib-ng/test/infcover.c:517
↓ 22 callersFunctionunlink
ext/include/boost/multi_index/sequenced_index.hpp:916
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