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github.com/deweylab/RSEM
/ functions
Functions
5,402 in github.com/deweylab/RSEM
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Functions
5,402
◇
Types & classes
14,945
↓ 3,697 callers
Function
next
boost/fusion/iterator/next.hpp:56
↓ 532 callers
Method
begin
iterator support
boost/array.hpp:75
↓ 466 callers
Method
size
size is constant
boost/array.hpp:159
↓ 406 callers
Method
push_back
HitContainer.h:30
↓ 367 callers
Method
end
boost/array.hpp:79
↓ 265 callers
Function
evaluate_polynomial
boost/math/tools/rational.hpp:189
↓ 170 callers
Function
operator=
boost/fusion/container/vector/detail/vector_n.hpp:188
↓ 151 callers
Function
kputc
samtools-1.3/htslib-1.3/htslib/kstring.h:154
↓ 125 callers
Function
pow
boost/math/special_functions/pow.hpp:124
↓ 121 callers
Function
kputs
samtools-1.3/htslib-1.3/htslib/kstring.h:149
↓ 106 callers
Method
clear
HitContainer.h:19
↓ 102 callers
Function
init_from_sequence
boost/fusion/container/vector/detail/vector_n.hpp:97
↓ 101 callers
Function
hgetc
! @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 callers
Method
assign
assign one value to all elements
boost/array.hpp:185
↓ 87 callers
Function
kputsn
samtools-1.3/htslib-1.3/htslib/kstring.h:132
↓ 73 callers
Function
bam_hdr_destroy
samtools-1.3/htslib-1.3/sam.c:54
↓ 73 callers
Function
seed
Seeds a @c linear_feedback_shift_engine with the default seed. */
boost/random/linear_feedback_shift.hpp:87
↓ 66 callers
Function
bam_destroy1
samtools-1.3/htslib-1.3/sam.c:288
↓ 63 callers
Function
bcf_hdr_append
samtools-1.3/htslib-1.3/vcf.c:615
↓ 62 callers
Method
data
direct access to data (read-only)
boost/array.hpp:171
↓ 54 callers
Function
cram_free_block
* Frees a CRAM block, deallocating internal data too. */
samtools-1.3/htslib-1.3/cram/cram_io.c:1067
↓ 54 callers
Function
itf8_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 callers
Function
bam_aux_get
samtools-1.3/htslib-1.3/sam.c:1254
↓ 51 callers
Function
cram_free_compression_header
samtools-1.3/htslib-1.3/cram/cram_io.c:3304
↓ 50 callers
Function
bam_init1
samtools-1.3/htslib-1.3/sam.c:283
↓ 47 callers
Function
cnull
boost/tuple/detail/tuple_basic.hpp:52
↓ 47 callers
Function
sam_read1
samtools-1.3/htslib-1.3/sam.c:1017
↓ 47 callers
Function
sam_write1
samtools-1.3/htslib-1.3/sam.c:1187
↓ 47 callers
Function
swap
boost/utility/swap.hpp:49
↓ 46 callers
Function
error
samtools-1.3/stats.c:1351
↓ 46 callers
Function
itos
my_assert.h:12
↓ 46 callers
Function
ksprintf
samtools-1.3/htslib-1.3/kstring.c:52
↓ 45 callers
Function
fail
samtools-1.3/htslib-1.3/test/hfile.c:35
↓ 42 callers
Method
getReadLength
SingleRead.h:26
↓ 41 callers
Function
log1p
boost/math/special_functions/log1p.hpp:292
↓ 41 callers
Function
sam_hdr_read
samtools-1.3/htslib-1.3/sam.c:732
↓ 40 callers
Method
empty
once this function is called, "insert" cannot be called anymore
bc_aux.h:76
↓ 40 callers
Method
getAdjustedProb
RSPD.h:70
↓ 40 callers
Function
ignore_unused_variable_warning
boost/concept_check.hpp:47
↓ 40 callers
Function
safe_itf8_get
samtools-1.3/htslib-1.3/cram/cram_io.h:110
↓ 40 callers
Method
spAt
sp : start position
GroupInfo.h:23
↓ 39 callers
Function
SwapEndian_32
swaps endianness of 32-bit value 'in-place'
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamAux.h:160
↓ 39 callers
Function
SwapEndian_32
swaps endianness of 32-bit value 'in-place'
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamAux.h:160
↓ 39 callers
Method
size
Returns the size of the sequence. */
boost/random/seed_seq.hpp:107
↓ 38 callers
Function
error
samtools-1.3/htslib-1.3/tabix.c:51
↓ 38 callers
Function
kputw
samtools-1.3/htslib-1.3/htslib/kstring.h:201
↓ 37 callers
Function
cram_free_container
samtools-1.3/htslib-1.3/cram/cram_io.c:2856
↓ 36 callers
Function
bgzf_write
samtools-1.3/htslib-1.3/bgzf.c:769
↓ 36 callers
Function
cram_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 callers
Method
write
RSPD.h:171
↓ 35 callers
Function
bgzf_read
samtools-1.3/htslib-1.3/bgzf.c:548
↓ 35 callers
Method
get
boost/smart_ptr/detail/shared_ptr_nmt.hpp:126
↓ 34 callers
Function
cram_stats_add
samtools-1.3/htslib-1.3/cram/cram_stats.c:51
↓ 34 callers
Function
evaluate_rational
boost/math/tools/rational.hpp:281
↓ 34 callers
Method
size
boost/format/alt_sstream.hpp:156
↓ 33 callers
Function
cram_decoder_init
samtools-1.3/htslib-1.3/cram/cram_codecs.c:1754
↓ 33 callers
Function
cram_encoder_init
samtools-1.3/htslib-1.3/cram/cram_codecs.c:1782
↓ 33 callers
Method
end
boost/range/iterator_range_core.hpp:248
↓ 33 callers
Method
getTotLen
RefSeq.h:67
↓ 32 callers
Method
getProb
Profile.h:114
↓ 32 callers
Function
tgamma
boost/math/special_functions/gamma.hpp:1290
↓ 31 callers
Function
bgzf_close
samtools-1.3/htslib-1.3/bgzf.c:797
↓ 31 callers
Function
eq
boost/tuple/tuple_comparison.hpp:54
↓ 31 callers
Method
insert
bc_aux.h:62
↓ 30 callers
Function
cstrtos
my_assert.h:29
↓ 29 callers
Method
begin
boost/range/iterator_range_core.hpp:243
↓ 29 callers
Method
swap
boost/smart_ptr/detail/shared_ptr_nmt.hpp:141
↓ 28 callers
Function
BOOST_CONCEPT_USAGE
boost/concept_check.hpp:67
↓ 28 callers
Function
ed_swap_4p
samtools-1.3/htslib-1.3/htslib/hts.h:616
↓ 28 callers
Function
g
boost/math/special_functions/lanczos.hpp:162
↓ 28 callers
Function
hts_close
samtools-1.3/htslib-1.3/hts.c:792
↓ 28 callers
Function
kputc_
samtools-1.3/htslib-1.3/htslib/kstring.h:170
↓ 28 callers
Method
widen
gcc takes wchar..
boost/format/detail/workarounds_gcc-2_95.hpp:75
↓ 27 callers
Function
expint
boost/math/special_functions/expint.hpp:1613
↓ 27 callers
Function
fail
samtools-1.3/htslib-1.3/test/sam.c:37
↓ 26 callers
Function
bam_aux2i
samtools-1.3/htslib-1.3/sam.c:1280
↓ 26 callers
Function
print_error_errno
samtools-1.3/bamtk.c:89
↓ 25 callers
Function
cram_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 callers
Function
flen
* 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 callers
Function
itf8_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 callers
Function
throw_exception
boost/throw_exception.hpp:63
↓ 24 callers
Function
erf
boost/math/special_functions/erf.hpp:1043
↓ 24 callers
Method
getMaxL
LenDist.h:54
↓ 24 callers
Method
getMinL
LenDist.h:53
↓ 24 callers
Method
isLowQuality
Read.h:17
↓ 24 callers
Function
kputsn_
samtools-1.3/htslib-1.3/htslib/kstring.h:185
↓ 24 callers
Function
sum_series
boost/math/tools/series.hpp:24
↓ 23 callers
Function
beta
boost/math/special_functions/beta.hpp:1326
↓ 23 callers
Function
lgamma
boost/math/special_functions/gamma.hpp:1442
↓ 23 callers
Function
sam_hdr_write
samtools-1.3/htslib-1.3/sam.c:774
↓ 22 callers
Function
bcf_enc_size
samtools-1.3/htslib-1.3/htslib/vcf.h:825
↓ 22 callers
Function
bcf_unpack
samtools-1.3/htslib-1.3/vcf.c:2000
↓ 22 callers
Function
bgzf_open
samtools-1.3/htslib-1.3/bgzf.c:171
↓ 22 callers
Function
destroy
boost/optional/optional.hpp:436
↓ 22 callers
Method
get
Returns a reference to the value if this is initialized, otherwise, the behaviour is UNDEFINED No-throw
boost/optional/optional.hpp:630
↓ 21 callers
Function
bam_is_mapped
sam_utils.h:49
↓ 21 callers
Function
bcf_hdr_id2int
samtools-1.3/htslib-1.3/vcf.c:2193
↓ 21 callers
Function
hts_open
samtools-1.3/htslib-1.3/hts.c:418
↓ 21 callers
Function
itrunc
boost/math/special_functions/trunc.hpp:43
↓ 21 callers
Function
ks_str
samtools-1.3/htslib-1.3/htslib/kstring.h:110
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