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Functions40,422 in github.com/ablab/spades

⨍ Functions 40,422◇ Types & classes 24,500↳ Endpoints 21
↓ 128 callersMethodlength
src/common/assembly_graph/core/graph_core.hpp:652
↓ 128 callersFunctionp7_profile_Create
Function: p7_profile_Create() * Synopsis: Allocates a profile. * * Purpose: Allocates for a profile of up to <M> nodes, for digital *
ext/src/hmmer/src/p7_profile.c:51
↓ 127 callersFunctionop
ext/src/lexy/include/lexy/dsl/operator.hpp:197
↓ 127 callersFunctionremove
Windows CE doesn't have the remove C function.
ext/src/googletest/googletest/test/googletest-filepath-test.cc:57
↓ 127 callersMethodresize
src/common/assembly_graph/core/id_distributor.cpp:21
↓ 126 callersMethodint_id
src/test/debruijn/paired_info_test.cpp:48
↓ 125 callersMethodbegin
src/projects/ionhammer/HSeq.hpp:99
↓ 123 callersFunctionp7_hmmfile_Close
Function: p7_hmmfile_Close() * * Purpose: Closes an open HMM file <hfp>. * * Returns: (void) */
ext/src/hmmer/src/p7_hmmfile.c:430
↓ 122 callersFunctionesl_sq_CreateDigital
Function: esl_sq_CreateDigital() * Synopsis: Create a new, empty <ESL_SQ> in digital mode. * Incept: SRE, Tue Jan 9 16:42:35 2007 [Janelia] *
ext/src/easel/esl_sq.c:729
↓ 122 callersFunctionsmpMultAssign
Transpose flag of the right-hand side vector
ext/include/blaze/blaze/math/smp/hpx/DenseVector.h:490
↓ 121 callersMethodconjugate
src/common/alignment/gap_info.hpp:150
↓ 120 callersMethodapply
ext/src/lexy/include/lexy/dsl/bits.hpp:62
↓ 120 callersMethodformat
(self, contig, profile)
src/projects/mts/scripts/converters.py:30
↓ 120 callersFunctionp7_hmmfile_Open
Function: p7_hmmfile_Open() * Synopsis: Open an HMM file <filename>. * * Purpose: Open an HMM file <filename>, and prepare to read the first
ext/src/hmmer/src/p7_hmmfile.c:119
↓ 119 callersFunctionBinWrite
src/common/io/binary/binary.hpp:75
↓ 119 callersMethodcoverage
* Method returns average coverage of the edge */
src/common/assembly_graph/core/graph.hpp:69
↓ 119 callersMethodreset
Compile time row arguments
ext/include/blaze/blaze/math/views/row/Dense.h:1287
↓ 118 callersMethodindex
Type of the elements
ext/include/blaze/blaze/math/dense/InitializerIterator.h:358
↓ 118 callersFunctionisChecked
ext/include/blaze/blaze/math/views/Check.h:225
↓ 117 callersFunctionesl_opt_DisplayHelp
Function: esl_opt_DisplayHelp() * Synopsis: Formats one-line help for each option. * * Purpose: For each option in <go>, print one line of brie
ext/src/easel/esl_getopts.c:1137
↓ 117 callersFunctionp7_hmmfile_Read
Function: p7_hmmfile_Read() * * Purpose: Read the next HMM from open save file <hfp>, and * optionally return this newly allocated HM
ext/src/hmmer/src/p7_hmmfile.c:1130
↓ 116 callersMethodemplace_back
src/common/adt/small_pod_vector.hpp:609
↓ 116 callersFunctionesl_randomness_CreateFast
Function: esl_randomness_CreateFast() * Synopsis: Create the alternative fast generator. * * THIS FUNCTION IS DEPRECATED. USE esl_ran
ext/src/easel/esl_random.c:149
↓ 116 callersMethodsize
src/common/alignment/rna/ss_coverage.hpp:124
↓ 114 callersMethodsize
Returns the number of TestPartResult objects in the array.
ext/src/googletest/googletest/src/gtest-test-part.cc:80
↓ 113 callersMethodsubstr
ext/src/lexy/include/lexy/_detail/string_view.hpp:123
↓ 112 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/TSMatSMatSchurExpr.h:222
↓ 112 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/SMatTSMatSchurExpr.h:222
↓ 111 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/TSMatSMatSchurExpr.h:232
↓ 111 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/SMatTSMatSchurExpr.h:232
↓ 111 callersMethodempty
--------------------------------------------------------------- @brief returns true, if group has no children, false otherwise */
ext/include/clipp/clipp.h:3407
↓ 111 callersMethodsize
Compile time column arguments
ext/include/blaze/blaze/math/views/column/Dense.h:1213
↓ 110 callersMethodemplace_back
ext/include/llvm/Support/JSON.h:192
↓ 109 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/TSMatTDMatMultExpr.h:371
↓ 109 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/TSMatDMatMultExpr.h:371
↓ 109 callersMethodconjugate
src/projects/spades/domain_graph.hpp:141
↓ 109 callersMethodcount
src/projects/binspreader/id_map.hpp:110
↓ 109 callersFunctionisspace
ext/include/clipp/clipp.h:152
↓ 108 callersFunctionElementsAre
ext/src/googletest/googlemock/include/gmock/gmock-matchers.h:5364
↓ 108 callersFunctionesl_dmatrix_Destroy
Function: esl_dmatrix_Destroy() * * Purpose: Frees an <ESL_DMATRIX> object <A>. */
ext/src/easel/esl_dmatrix.c:142
↓ 108 callersMethodstring
ext/src/lexy/include/lexy/error.hpp:112
↓ 107 callersMethodEdgeNucls
src/common/auxiliary_graphs/contracted_graph/contracted_graph.cpp:110
↓ 107 callersFunctionabs
Transpose flag
ext/include/blaze/blaze/math/expressions/DVecMapExpr.h:1298
↓ 107 callersFunctionceil
ext/include/blaze/blaze/math/proxy/Proxy.h:1128
↓ 107 callersFunctionldexp
ext/include/boost/math/ccmath/ldexp.hpp:45
↓ 106 callersFunctiondestroy
ext/include/blaze/blaze/util/algorithms/Destroy.h:67
↓ 106 callersMethodend
src/common/adt/bag.hpp:83
↓ 106 callersMethodreal
Type of the complex number
ext/include/blaze/blaze/math/proxy/ComplexProxy.h:137
↓ 105 callersFunctionfloat
Positive infinity type
ext/include/blaze/blaze/math/Infinity.h:280
↓ 103 callersFunctionconj
Transpose flag
ext/include/blaze/blaze/math/expressions/DVecMapExpr.h:1466
↓ 103 callersMethodcount
Getters for the number of values stored in this node.
ext/include/parallel_hashmap/btree.h:1180
↓ 102 callersFunctionmap
Type of the custom operation
ext/include/blaze/blaze/math/expressions/DVecMapExpr.h:1100
↓ 102 callersMethodsize
Type of the condition variable
ext/include/blaze/blaze/math/smp/threads/ThreadBackend.h:209
↓ 101 callersMethoddata
ext/src/lexy/include/lexy/lexeme.hpp:54
↓ 100 callersFunctionaddressof
ext/include/boost/core/addressof.hpp:37
↓ 100 callersFunctionesl_sq_Reuse
Function: esl_sq_Reuse() * Synopsis: Reinitialize an <ESL_SQ> for re-use. * Incept: SRE, Thu Dec 23 12:23:51 2004 [Zaragoza] * * Purpose: G
ext/src/easel/esl_sq.c:442
↓ 100 callersMethodreserve
Compile time row arguments
ext/include/blaze/blaze/math/views/row/Sparse.h:1347
↓ 99 callersMethodrows
Compile time column arguments
ext/include/blaze/blaze/math/views/columns/Dense.h:1458
↓ 98 callersFunctionGe
Creates a polymorphic matcher that matches a 2-tuple where the first field >= the second field.
ext/src/googletest/googlemock/include/gmock/gmock-matchers.h:4856
↓ 98 callersFunctioncheckAlignment
ext/include/blaze/blaze/util/AlignmentCheck.h:68
↓ 98 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/DMatTDMatMapExpr.h:244
↓ 98 callersFunctioncopy
ext/include/folly/Utility.h:123
↓ 98 callersFunctionesl_stopwatch_Destroy
Function: esl_stopwatch_Destroy() * * Purpose: Frees an <ESL_STOPWATCH>. */
ext/src/easel/esl_stopwatch.c:52
↓ 98 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/DMatTDMatMapExpr.h:234
↓ 98 callersFunctionunview
Compile time row arguments
ext/include/blaze/blaze/math/views/Row.h:2259
↓ 97 callersFunctionesl_stopwatch_Create
Function: esl_stopwatch_Create() * * Purpose: Creates a new stopwatch. * * Returns: ptr to a new <ESL_STOPWATCH> object; caller is *
ext/src/easel/esl_stopwatch.c:31
↓ 96 callersMethodimpl
ext/include/boost/multi_index/detail/ord_index_node.hpp:623
↓ 95 callersFunctionbegin
ext/include/llvm/ADT/ArrayRef.h:144
↓ 95 callersMethodcolumns
Remaining column indices
ext/include/blaze/blaze/math/views/columns/ColumnsData.h:233
↓ 95 callersFunctionesl_getopts_CreateDefaultApp
Function: esl_getopts_CreateDefaultApp() * Synopsis: Initialize a standard Easel application. * * Purpose: Carry out the usual sequence of even
ext/src/easel/esl_getopts.c:198
↓ 95 callersMethodimag
Type of the complex number
ext/include/blaze/blaze/math/proxy/ComplexProxy.h:174
↓ 95 callersMethodinsert
src/common/modules/path_extend/scaff_supplementary.hpp:140
↓ 95 callersMethodsubstr
Return a reference to the substring from [Start, Start + N). \param Start The index of the starting character in the substring; if the index is npos
ext/include/llvm/ADT/SmallString.h:245
↓ 94 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/TSMatSMatMultExpr.h:277
↓ 94 callersFunctionp7_oprofile_Destroy
Function: p7_oprofile_Destroy() * Synopsis: Frees an optimized profile structure. * Incept: SRE, Sun Nov 25 12:22:21 2007 [Casa de Gatos] */
ext/src/hmmer/src/impl_vmx/p7_oprofile.c:172
↓ 94 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/TDMatSMatMultExpr.h:360
↓ 94 callersFunctionwrite_str
ext/src/lexy/include/lexy/visualize.hpp:94
↓ 93 callersFunction_mm_mul_ps
Multiplies the four single-precision, floating-point values of a and b. r0 := a0 * b0 r1 := a1 * b1 r2 := a2 * b2 r3 := a3 * b3 https://msdn.microso
ext/include/sse2neon/sse2neon.h:2190
↓ 93 callersMethodnonZeros
NonZeros function !\brief Returns the number of non-zero elements in the sparse vector. // // \return The number of non-zero elements in the spa
ext/include/blaze/blaze/math/expressions/SVecMapExpr.h:368
↓ 93 callersFunctionround
src/common/math/xmath.h:331
↓ 92 callersMethodAt
src/common/assembly_graph/paths/bidirectional_path.hpp:192
↓ 92 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/TSMatTSMatMultExpr.h:278
↓ 92 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/SMatDMatMultExpr.h:392
↓ 92 callersFunctionerase
Type tag
ext/include/blaze/blaze/math/sparse/ZeroVector.h:993
↓ 92 callersMethodload
Compile time subvector arguments
ext/include/blaze/blaze/math/views/subvector/Dense.h:1886
↓ 92 callersMethodload
Compile time column arguments
ext/include/blaze/blaze/math/views/column/Dense.h:1512
↓ 92 callersMethodload
Compile time row arguments
ext/include/blaze/blaze/math/views/row/Dense.h:1513
↓ 92 callersMethodpush_back
src/projects/spades_tools/kmercount.cpp:92
↓ 92 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/SMatSMatMultExpr.h:267
↓ 91 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/SMatSMatMultExpr.h:277
↓ 91 callersFunctionesl_tmpfile_named
Function: esl_tmpfile_named() * * Purpose: Open a persistent temporary file relative to the current * working directory. The file nam
ext/src/easel/easel.c:2196
↓ 91 callersFunctionisdigit
ext/include/clipp/clipp.h:155
↓ 91 callersFunctionp7_FLogsum
Function: p7_FLogsum() * Synopsis: Approximate $\log(e^a + e^b)$. * * Purpose: Returns a fast table-driven approximation to * $\log
ext/src/hmmer/src/logsum.c:104
↓ 91 callersMethodparent
ext/include/boost/multi_index/detail/ord_index_node.hpp:616
↓ 91 callersMethodpeek
(self, index=0)
ext/src/python_libs/pyyaml3/reader.py:87
↓ 91 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/TSMatTSMatMultExpr.h:268
↓ 91 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/TDMatTSMatMultExpr.h:382
↓ 91 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/TSMatSMatMultExpr.h:267
↓ 90 callersMethodLengthAt
Length from beginning of i-th edge to path end for forward directed path: L(e1 + e2 + ... + eN)
src/common/assembly_graph/paths/bidirectional_path.hpp:569
↓ 90 callersMethodend
src/common/modules/path_extend/pe_utils.hpp:168
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