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github.com/ablab/spades
/ functions
Functions
40,422 in github.com/ablab/spades
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Functions
40,422
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Types & classes
24,500
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Endpoints
21
↓ 17 callers
Method
position
The corresponding position, rounded down to the previous column start.
ext/src/lexy/include/lexy/input_location.hpp:165
↓ 17 callers
Method
rend
src/common/adt/flat_map.hpp:60
↓ 17 callers
Method
rightOperand
Right operand access !\brief Returns the right-hand side dense matrix operand. // // \return The right-hand side dense matrix operand. */
ext/include/blaze/blaze/math/expressions/DMatDMatMultExpr.h:441
↓ 17 callers
Method
rightOperand
Right operand access !\brief Returns the right-hand side transpose dense matrix operand. // // \return The right-hand side transpose dense matri
ext/include/blaze/blaze/math/expressions/TDMatTDMatMultExpr.h:439
↓ 17 callers
Method
scale
ext/include/boost/math/distributions/pareto.hpp:150
↓ 17 callers
Method
scale
Data type of the scalar value
ext/include/blaze/blaze/math/proxy/DenseMatrixProxy.h:681
↓ 17 callers
Method
size
ext/include/tsl/htrie_hash.h:964
↓ 17 callers
Function
spacing
Storage order of the matrix
ext/include/blaze/blaze/math/expressions/DenseMatrix.h:265
↓ 17 callers
Method
stop
src/common/utils/perf/perfcounter.hpp:75
↓ 17 callers
Function
swap
ext/include/boost/multi_index/detail/auto_space.hpp:94
↓ 17 callers
Method
trim
src/projects/pathracer/pathtree.hpp:280
↓ 17 callers
Function
tryAddAssign
Type of the right-hand side vector
ext/include/blaze/blaze/math/views/Row.h:1888
↓ 17 callers
Function
trySubAssign
Type of the right-hand side vector
ext/include/blaze/blaze/math/views/Row.h:1921
↓ 17 callers
Function
type
Gets the outcome of the test part.
ext/src/googletest/googletest/include/gtest/gtest-test-part.h:77
↓ 17 callers
Function
yamlize
ext/include/llvm/Support/YAMLTraits.h:1002
↓ 17 callers
Function
zng_alloc
Function to allocate 16 or 64-byte aligned memory */
ext/src/zlib-ng/zutil_p.h:18
↓ 16 callers
Function
ArrayEq
ext/src/googletest/googletest/include/gtest/internal/gtest-internal.h:991
↓ 16 callers
Method
Bar
ext/src/googletest/googletest/test/gtest_unittest.cc:5022
↓ 16 callers
Method
Conjugate
src/common/assembly_graph/paths/bidirectional_path.hpp:94
↓ 16 callers
Function
CountIf
ext/src/googletest/googletest/src/gtest-internal-inl.h:276
↓ 16 callers
Method
DeleteEdge
src/common/assembly_graph/core/observable_graph.hpp:200
↓ 16 callers
Function
EndsWith
ext/src/googletest/googlemock/include/gmock/gmock-matchers.h:4789
↓ 16 callers
Function
Factorial
Returns n! (the factorial of n). For negative n, n! is defined to be 1.
ext/src/googletest/googletest/samples/sample1.cc:35
↓ 16 callers
Function
GetEnv
ext/src/googletest/googletest/include/gtest/internal/gtest-port.h:2138
↓ 16 callers
Function
GetTestsForAllIterations
Runs the test program and returns a list of test lists. Args: extra_env: a map from environment variables to their values args: command lin
ext/src/googletest/googletest/test/googletest-shuffle-test.py:85
↓ 16 callers
Function
IsAsciiWordChar
ext/src/googletest/googletest/src/gtest-port.cc:769
↓ 16 callers
Function
IsHalfOf
ext/src/googletest/googlemock/test/gmock-matchers-containers_test.cc:2557
↓ 16 callers
Method
IsSubpath
src/common/modules/path_extend/overlap_remover.cpp:75
↓ 16 callers
Function
IsTrue
ext/src/googletest/googletest/src/gtest.cc:6484
↓ 16 callers
Function
ShouldShard
Checks whether sharding is enabled by examining the relevant environment variable values. If the variables are present, but inconsistent (i.e., shard_
ext/src/googletest/googletest/src/gtest.cc:6168
↓ 16 callers
Method
Size
src/projects/ionhammer/read_corrector_structs_new.h:71
↓ 16 callers
Function
StrCaseEq
ext/src/googletest/googlemock/include/gmock/gmock-matchers.h:4756
↓ 16 callers
Function
WhenSorted
ext/src/googletest/googlemock/include/gmock/gmock-matchers.h:4988
↓ 16 callers
Method
With
ext/src/googletest/googlemock/include/gmock/gmock-spec-builders.h:1551
↓ 16 callers
Function
_mi_thread_id
ext/src/mimalloc/include/mimalloc-internal.h:801
↓ 16 callers
Function
_mm_cmpgt_ps
Compares for greater than. r0 := (a0 > b0) ? 0xffffffff : 0x0 r1 := (a1 > b1) ? 0xffffffff : 0x0 r2 := (a2 > b2) ? 0xffffffff : 0x0 r3 := (a3 > b3) ?
ext/include/sse2neon/sse2neon.h:1139
↓ 16 callers
Function
_mm_cvtsi128_si32
Copy the lower 32-bit integer in a to dst. dst[31:0] := a[31:0] https://software.intel.com/sites/landingpage/IntrinsicsGuide/#text=_mm_cvtsi128_si32
ext/include/sse2neon/sse2neon.h:4171
↓ 16 callers
Function
_mm_cvtsi32_si128
Moves 32-bit integer a to the least significant 32 bits of an __m128 object, zero extending the upper bits. r0 := a r1 := 0x0 r2 := 0x0 r3 := 0x0 ht
ext/include/sse2neon/sse2neon.h:4222
↓ 16 callers
Method
back
src/common/assembly_graph/paths/mapping_path.hpp:248
↓ 16 callers
Method
begin
Operations
ext/include/boost/algorithm/string/detail/util.hpp:45
↓ 16 callers
Method
begin
Type tag
ext/include/blaze/blaze/math/dense/StaticMatrix.h:1261
↓ 16 callers
Method
begin
Type tag
ext/include/blaze/blaze/math/dense/HybridMatrix.h:1321
↓ 16 callers
Function
bgzf_close
ext/src/samtools/bgzf.c:570
↓ 16 callers
Function
broadcast
src/projects/hpcspades/mpi/pipeline/partask_mpi.hpp:173
↓ 16 callers
Function
buffer_refill
buffer_refill() * For current buffer position bf->pos, try to assure that * we have at least <bf->pagesize> bytes loaded in <bf->mem> to parse
ext/src/easel/esl_buffer.c:1679
↓ 16 callers
Method
canAlias
Data type of the foreign expression
ext/include/blaze/blaze/math/views/subvector/Dense.h:1737
↓ 16 callers
Method
columns
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/DMatRepeatExpr.h:181
↓ 16 callers
Method
columns
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/SMatRepeatExpr.h:179
↓ 16 callers
Method
data
src/common/sequence/rtseq.hpp:662
↓ 16 callers
Method
data
src/common/io/kmers/mmapped_reader.hpp:224
↓ 16 callers
Function
distance
src/projects/ionhammer/hkmer_distance.hpp:334
↓ 16 callers
Method
empty
Return true if the SparseBitVector is empty
ext/include/llvm/ADT/SparseBitVector.h:795
↓ 16 callers
Method
end
src/common/assembly_graph/core/graph_iterators.hpp:529
↓ 16 callers
Method
end
Type tag
ext/include/blaze/blaze/math/dense/StaticMatrix.h:1342
↓ 16 callers
Method
end
Type tag
ext/include/blaze/blaze/math/dense/HybridMatrix.h:1402
↓ 16 callers
Method
end
Compile time column arguments
ext/include/blaze/blaze/math/views/columns/Dense.h:758
↓ 16 callers
Function
erfc_inv
ext/include/boost/math/special_functions/detail/erf_inv.hpp:398
↓ 16 callers
Function
err_fclose
ext/src/bwa/utils.c:260
↓ 16 callers
Function
esl_abc_FExpectScVec
ext/src/easel/esl_alphabet.c:1581
↓ 16 callers
Function
esl_fileparser_GetToken
Function: esl_fileparser_GetToken() * Incept: SRE, Fri Jul 9 13:03:50 2004 [St. Louis] * * Purpose: Sets a pointer to the next field in the
ext/src/easel/esl_fileparser.c:199
↓ 16 callers
Function
esl_fileparser_Open
Function: esl_fileparser_Open() * Incept: SRE, Tue Apr 3 08:09:56 2007 [Janelia] * * Purpose: Opens <filename> for reading. * *
ext/src/easel/esl_fileparser.c:57
↓ 16 callers
Function
esl_free
Function: esl_free() * Synopsis: free(), while allowing ptr to be NULL. * Incept: SRE, Fri Nov 3 17:12:01 2017 * * Purpose: Easel uses a c
ext/src/easel/easel.c:470
↓ 16 callers
Function
esl_histogram_CreateFull
Function: esl_histogram_CreateFull() * Synopsis: A <ESL_HISTOGRAM> to keep all data samples. * * Purpose: Alternative form of <esl_histogram_Cr
ext/src/easel/esl_histogram.c:136
↓ 16 callers
Function
esl_keyhash_Create
Function: esl_keyhash_Create() * Synopsis: Allocates a new keyhash. * * Purpose: Create a new hash table for key indexing, and returns *
ext/src/easel/esl_keyhash.c:45
↓ 16 callers
Function
esl_msa_Digitize
Function: esl_msa_Digitize() * Synopsis: Digitizes an msa, converting it from text mode. * * Purpose: Given an alignment <msa> in text mode, co
ext/src/easel/esl_msa.c:874
↓ 16 callers
Function
esl_rand64_Create
Function: esl_rand64_Create() * Synopsis: Create a 64-bit Mersenne Twister RNG. * Incept: SRE, Tue 21 Aug 2018 * * Purpose: Create a new RN
ext/src/easel/esl_rand64.c:92
↓ 16 callers
Function
esl_rootfinder_Destroy
ext/src/easel/esl_rootfinder.c:200
↓ 16 callers
Function
esl_sq_SetName
Function: esl_sq_SetName() * Synopsis: Set the name of a sequence. * Incept: SRE, Thu Jan 11 08:42:53 2007 [Janelia] * * Purpose: Set the n
ext/src/easel/esl_sq.c:1048
↓ 16 callers
Function
esl_stats_LogGamma
Function: esl_stats_LogGamma() * Synopsis: Calculates $\log \Gamma(x)$. * * Purpose: Returns natural log of $\Gamma(x)$, for $x > 0$. * * Cr
ext/src/easel/esl_stats.c:118
↓ 16 callers
Function
esl_tree_Destroy
Function: esl_tree_Destroy() * * Purpose: Frees an <ESL_TREE> object. */
ext/src/easel/esl_tree.c:613
↓ 16 callers
Function
esl_vec_DNorm
Function: esl_vec_{DF}Norm() * Synopsis: Normalize probability vector. * * Purpose: Normalizes a probability vector <vec>, *
ext/src/easel/esl_vectorops.c:1141
↓ 16 callers
Function
esl_vmx_set_float
Function: esl_vmx_set_float() * Synopsis: Fills float vector with x. * * Purpose: Sets all elements in the vector <float> to x. */
ext/src/easel/esl_vmx.h:24
↓ 16 callers
Method
execute
(self, commands)
src/projects/spades/pipeline/spades_pipeline/executors/executor_mpi.py:19
↓ 16 callers
Function
g
()
src/tools/webvis/static/sigma.min.js:2
↓ 16 callers
Method
get_commands
(self, cfg)
src/projects/spades/pipeline/spades_pipeline/stages/pipeline.py:38
↓ 16 callers
Method
get_value
src/common/assembly_graph/index/edge_position_index.hpp:127
↓ 16 callers
Function
h
(e)
src/tools/webvis/static/jquery-ui.min.js:6
↓ 16 callers
Method
insert
ext/include/boost/property_tree/detail/ptree_implementation.hpp:326
↓ 16 callers
Function
isIntact
Type tag
ext/include/blaze/blaze/math/dense/HybridVector.h:3075
↓ 16 callers
Function
isIntact
Type tag
ext/include/blaze/blaze/math/dense/DynamicVector.h:2947
↓ 16 callers
Function
isZero
ext/include/blaze/blaze/math/proxy/Proxy.h:2227
↓ 16 callers
Function
key_compare
ext/src/nlopt/isres/isres.c:48
↓ 16 callers
Method
kill
(self, job_name)
src/projects/spades/pipeline/spades_pipeline/executors/executor_local.py:86
↓ 16 callers
Function
last_finder
ext/include/boost/algorithm/string/finder.hpp:89
↓ 16 callers
Function
make_temp_dir
src/common/utils/filesystem/temporary.hpp:103
↓ 16 callers
Function
mi_stat_print
ext/src/mimalloc/src/stats.c:173
↓ 16 callers
Function
modify_metadata
ext/src/gqf/gqf.c:173
↓ 16 callers
Method
offset
ext/include/parallel_hashmap/phmap.h:153
↓ 16 callers
Method
on
ext/src/lexy/include/lexy/action/base.hpp:155
↓ 16 callers
Function
p7_builder_Destroy
Function: p7_builder_Destroy() * Synopsis: Free a <P7_BUILDER> * * Purpose: Frees a <P7_BUILDER> object. */
ext/src/hmmer/src/p7_builder.c:347
↓ 16 callers
Function
p7_trace_Score
Function: p7_trace_Score() * Incept: SRE, Tue Mar 6 14:40:34 2007 [Janelia] * * Purpose: Score path <tr> for digital target sequence <dsq>
ext/src/hmmer/src/p7_trace.c:872
↓ 16 callers
Function
parse_integer
Function: parse_integer() * Synopsis: Parse an integer * Incept: MSF, Mon Dec 10, 2009 [Janelia] * * Purpose: Reads an integer from the hea
ext/src/easel/esl_sqio_ncbi.c:3245
↓ 16 callers
Method
path
src/common/alignment/pacbio/gap_dijkstra.hpp:168
↓ 16 callers
Method
pattern
Matches every identifier, ignoring reserved ones.
ext/src/lexy/include/lexy/dsl/identifier.hpp:270
↓ 16 callers
Function
pow2
ext/include/blaze/blaze/math/proxy/Proxy.h:1468
↓ 16 callers
Method
push
src/common/adt/queue_iterator.hpp:287
↓ 16 callers
Function
raise_evaluation_error
ext/include/boost/math/policies/error_handling.hpp:497
↓ 16 callers
Method
reached
src/common/assembly_graph/dijkstra/dijkstra_algorithm.hpp:261
↓ 16 callers
Method
read
Type of the array elements
ext/include/blaze/blaze/util/serialization/Archive.h:423
↓ 16 callers
Method
remove
ext/src/lexy/include/lexy/dsl/char_class.hpp:67
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