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Functions5,402 in github.com/deweylab/RSEM

↓ 3,697 callersFunctionnext
boost/fusion/iterator/next.hpp:56
↓ 532 callersMethodbegin
iterator support
boost/array.hpp:75
↓ 466 callersMethodsize
size is constant
boost/array.hpp:159
↓ 406 callersMethodpush_back
HitContainer.h:30
↓ 367 callersMethodend
boost/array.hpp:79
↓ 265 callersFunctionevaluate_polynomial
boost/math/tools/rational.hpp:189
↓ 170 callersFunctionoperator=
boost/fusion/container/vector/detail/vector_n.hpp:188
↓ 151 callersFunctionkputc
samtools-1.3/htslib-1.3/htslib/kstring.h:154
↓ 125 callersFunctionpow
boost/math/special_functions/pow.hpp:124
↓ 121 callersFunctionkputs
samtools-1.3/htslib-1.3/htslib/kstring.h:149
↓ 106 callersMethodclear
HitContainer.h:19
↓ 102 callersFunctioninit_from_sequence
boost/fusion/container/vector/detail/vector_n.hpp:97
↓ 101 callersFunctionhgetc
! @abstract Read one character from the stream @return The character read, or EOF on end-of-file or error */
samtools-1.3/htslib-1.3/htslib/hfile.h:124
↓ 95 callersMethodassign
assign one value to all elements
boost/array.hpp:185
↓ 87 callersFunctionkputsn
samtools-1.3/htslib-1.3/htslib/kstring.h:132
↓ 73 callersFunctionbam_hdr_destroy
samtools-1.3/htslib-1.3/sam.c:54
↓ 73 callersFunctionseed
Seeds a @c linear_feedback_shift_engine with the default seed. */
boost/random/linear_feedback_shift.hpp:87
↓ 66 callersFunctionbam_destroy1
samtools-1.3/htslib-1.3/sam.c:288
↓ 63 callersFunctionbcf_hdr_append
samtools-1.3/htslib-1.3/vcf.c:615
↓ 62 callersMethoddata
direct access to data (read-only)
boost/array.hpp:171
↓ 54 callersFunctioncram_free_block
* Frees a CRAM block, deallocating internal data too. */
samtools-1.3/htslib-1.3/cram/cram_io.c:1067
↓ 54 callersFunctionitf8_put
* Stores a value to memory in ITF-8 format. * * Returns the number of bytes required to store the number. * This is a maximum of 5 bytes. */
samtools-1.3/htslib-1.3/cram/cram_io.c:278
↓ 52 callersFunctionbam_aux_get
samtools-1.3/htslib-1.3/sam.c:1254
↓ 51 callersFunctioncram_free_compression_header
samtools-1.3/htslib-1.3/cram/cram_io.c:3304
↓ 50 callersFunctionbam_init1
samtools-1.3/htslib-1.3/sam.c:283
↓ 47 callersFunctioncnull
boost/tuple/detail/tuple_basic.hpp:52
↓ 47 callersFunctionsam_read1
samtools-1.3/htslib-1.3/sam.c:1017
↓ 47 callersFunctionsam_write1
samtools-1.3/htslib-1.3/sam.c:1187
↓ 47 callersFunctionswap
boost/utility/swap.hpp:49
↓ 46 callersFunctionerror
samtools-1.3/stats.c:1351
↓ 46 callersFunctionitos
my_assert.h:12
↓ 46 callersFunctionksprintf
samtools-1.3/htslib-1.3/kstring.c:52
↓ 45 callersFunctionfail
samtools-1.3/htslib-1.3/test/hfile.c:35
↓ 42 callersMethodgetReadLength
SingleRead.h:26
↓ 41 callersFunctionlog1p
boost/math/special_functions/log1p.hpp:292
↓ 41 callersFunctionsam_hdr_read
samtools-1.3/htslib-1.3/sam.c:732
↓ 40 callersMethodempty
once this function is called, "insert" cannot be called anymore
bc_aux.h:76
↓ 40 callersMethodgetAdjustedProb
RSPD.h:70
↓ 40 callersFunctionignore_unused_variable_warning
boost/concept_check.hpp:47
↓ 40 callersFunctionsafe_itf8_get
samtools-1.3/htslib-1.3/cram/cram_io.h:110
↓ 40 callersMethodspAt
sp : start position
GroupInfo.h:23
↓ 39 callersFunctionSwapEndian_32
swaps endianness of 32-bit value 'in-place'
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamAux.h:160
↓ 39 callersFunctionSwapEndian_32
swaps endianness of 32-bit value 'in-place'
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamAux.h:160
↓ 39 callersMethodsize
Returns the size of the sequence. */
boost/random/seed_seq.hpp:107
↓ 38 callersFunctionerror
samtools-1.3/htslib-1.3/tabix.c:51
↓ 38 callersFunctionkputw
samtools-1.3/htslib-1.3/htslib/kstring.h:201
↓ 37 callersFunctioncram_free_container
samtools-1.3/htslib-1.3/cram/cram_io.c:2856
↓ 36 callersFunctionbgzf_write
samtools-1.3/htslib-1.3/bgzf.c:769
↓ 36 callersFunctioncram_new_block
* Allocates a new cram_block structure with a specified content_type and * id. * * Returns block pointer on success * NULL on failure */
samtools-1.3/htslib-1.3/cram/cram_io.c:913
↓ 36 callersMethodwrite
RSPD.h:171
↓ 35 callersFunctionbgzf_read
samtools-1.3/htslib-1.3/bgzf.c:548
↓ 35 callersMethodget
boost/smart_ptr/detail/shared_ptr_nmt.hpp:126
↓ 34 callersFunctioncram_stats_add
samtools-1.3/htslib-1.3/cram/cram_stats.c:51
↓ 34 callersFunctionevaluate_rational
boost/math/tools/rational.hpp:281
↓ 34 callersMethodsize
boost/format/alt_sstream.hpp:156
↓ 33 callersFunctioncram_decoder_init
samtools-1.3/htslib-1.3/cram/cram_codecs.c:1754
↓ 33 callersFunctioncram_encoder_init
samtools-1.3/htslib-1.3/cram/cram_codecs.c:1782
↓ 33 callersMethodend
boost/range/iterator_range_core.hpp:248
↓ 33 callersMethodgetTotLen
RefSeq.h:67
↓ 32 callersMethodgetProb
Profile.h:114
↓ 32 callersFunctiontgamma
boost/math/special_functions/gamma.hpp:1290
↓ 31 callersFunctionbgzf_close
samtools-1.3/htslib-1.3/bgzf.c:797
↓ 31 callersFunctioneq
boost/tuple/tuple_comparison.hpp:54
↓ 31 callersMethodinsert
bc_aux.h:62
↓ 30 callersFunctioncstrtos
my_assert.h:29
↓ 29 callersMethodbegin
boost/range/iterator_range_core.hpp:243
↓ 29 callersMethodswap
boost/smart_ptr/detail/shared_ptr_nmt.hpp:141
↓ 28 callersFunctionBOOST_CONCEPT_USAGE
boost/concept_check.hpp:67
↓ 28 callersFunctioned_swap_4p
samtools-1.3/htslib-1.3/htslib/hts.h:616
↓ 28 callersFunctiong
boost/math/special_functions/lanczos.hpp:162
↓ 28 callersFunctionhts_close
samtools-1.3/htslib-1.3/hts.c:792
↓ 28 callersFunctionkputc_
samtools-1.3/htslib-1.3/htslib/kstring.h:170
↓ 28 callersMethodwiden
gcc takes wchar..
boost/format/detail/workarounds_gcc-2_95.hpp:75
↓ 27 callersFunctionexpint
boost/math/special_functions/expint.hpp:1613
↓ 27 callersFunctionfail
samtools-1.3/htslib-1.3/test/sam.c:37
↓ 26 callersFunctionbam_aux2i
samtools-1.3/htslib-1.3/sam.c:1280
↓ 26 callersFunctionprint_error_errno
samtools-1.3/bamtk.c:89
↓ 25 callersFunctioncram_stats_encoding
* Computes entropy from integer frequencies for various encoding methods and * picks the best encoding. * * FIXME: we could reuse some of the code
samtools-1.3/htslib-1.3/cram/cram_stats.c:147
↓ 25 callersFunctionflen
* vlen: 27/10/95 written by James Bonfield, jkb@mrc-lmb.cam.ac.uk * * Given sprintf style of arguments this routine returns the maximum * size of b
samtools-1.3/htslib-1.3/cram/vlen.c:106
↓ 25 callersFunctionitf8_put_blk
* Pushes a value in ITF8 format onto the end of a block. * This shouldn't be used for high-volume data as it is not the fastest * method. * * Retu
samtools-1.3/htslib-1.3/cram/cram_io.c:626
↓ 25 callersFunctionthrow_exception
boost/throw_exception.hpp:63
↓ 24 callersFunctionerf
boost/math/special_functions/erf.hpp:1043
↓ 24 callersMethodgetMaxL
LenDist.h:54
↓ 24 callersMethodgetMinL
LenDist.h:53
↓ 24 callersMethodisLowQuality
Read.h:17
↓ 24 callersFunctionkputsn_
samtools-1.3/htslib-1.3/htslib/kstring.h:185
↓ 24 callersFunctionsum_series
boost/math/tools/series.hpp:24
↓ 23 callersFunctionbeta
boost/math/special_functions/beta.hpp:1326
↓ 23 callersFunctionlgamma
boost/math/special_functions/gamma.hpp:1442
↓ 23 callersFunctionsam_hdr_write
samtools-1.3/htslib-1.3/sam.c:774
↓ 22 callersFunctionbcf_enc_size
samtools-1.3/htslib-1.3/htslib/vcf.h:825
↓ 22 callersFunctionbcf_unpack
samtools-1.3/htslib-1.3/vcf.c:2000
↓ 22 callersFunctionbgzf_open
samtools-1.3/htslib-1.3/bgzf.c:171
↓ 22 callersFunctiondestroy
boost/optional/optional.hpp:436
↓ 22 callersMethodget
Returns a reference to the value if this is initialized, otherwise, the behaviour is UNDEFINED No-throw
boost/optional/optional.hpp:630
↓ 21 callersFunctionbam_is_mapped
sam_utils.h:49
↓ 21 callersFunctionbcf_hdr_id2int
samtools-1.3/htslib-1.3/vcf.c:2193
↓ 21 callersFunctionhts_open
samtools-1.3/htslib-1.3/hts.c:418
↓ 21 callersFunctionitrunc
boost/math/special_functions/trunc.hpp:43
↓ 21 callersFunctionks_str
samtools-1.3/htslib-1.3/htslib/kstring.h:110
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