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Functions5,402 in github.com/deweylab/RSEM

⨍ Functions 5,402◇ Types & classes 14,945
↓ 10 callersFunctionmake_tuple
boost/tuple/detail/tuple_basic_no_partial_spec.hpp:570
↓ 10 callersFunctionmake_tuple
boost/fusion/tuple/make_tuple.hpp:19
↓ 10 callersFunctionmaybe_throw_exception
auxiliary func called by parse_printf_directive for centralising error handling it either throws if user sets the corresponding flag, or does nothing.
boost/format/parsing.hpp:104
↓ 10 callersFunctionregidx_overlap
samtools-1.3/htslib-1.3/regidx.c:244
↓ 10 callersFunctionrequire_boolean_expr
boost/concept_check.hpp:229
↓ 10 callersFunctionround
boost/math/special_functions/round.hpp:20
↓ 10 callersFunctionsam_index_load
samtools-1.3/htslib-1.3/sam.c:600
↓ 9 callersFunctionBOOST_MATH_META_INT
boost/math/policies/policy.hpp:217
↓ 9 callersFunctionSwapEndian_64
swaps endianness of 64-bit value 'in-place'
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamAux.h:177
↓ 9 callersFunctionSwapEndian_64
swaps endianness of 64-bit value 'in-place'
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamAux.h:177
↓ 9 callersFunctionassign
Assigns from another optional<T> (deep-copies the rhs value)
boost/optional/optional.hpp:271
↓ 9 callersFunctionbcf_enc_vint
samtools-1.3/htslib-1.3/vcf.c:1416
↓ 9 callersFunctioncram_get_block_by_id
samtools-1.3/htslib-1.3/cram/cram_io.h:243
↓ 9 callersFunctioncram_major_vers
samtools-1.3/htslib-1.3/cram/cram_external.c:56
↓ 9 callersFunctioncram_read_container
* Reads a container header. * * Returns cram_container on success * NULL on failure or no container left (fd->err == 0). */
samtools-1.3/htslib-1.3/cram/cram_io.c:2898
↓ 9 callersFunctioned_is_big
samtools-1.3/htslib-1.3/htslib/hts.h:597
↓ 9 callersFunctionfai_load
samtools-1.3/htslib-1.3/faidx.c:288
↓ 9 callersFunctionfloat_distance
boost/math/special_functions/next.hpp:377
↓ 9 callersFunctionfmod_workaround
boost/math/tools/workaround.hpp:22
↓ 9 callersMethodgetConPrb
SingleHit.h:30
↓ 9 callersMethodgetInsertL
PairedEndHit.h:18
↓ 9 callersFunctionhclose_abruptly
samtools-1.3/htslib-1.3/hfile.c:317
↓ 9 callersFunctionhfile_add_scheme_handler
samtools-1.3/htslib-1.3/hfile.c:608
↓ 9 callersFunctionhts_md5_destroy
samtools-1.3/htslib-1.3/md5.c:370
↓ 9 callersFunctionowens_t_znorm2
boost/math/special_functions/owens_t.hpp:45
↓ 9 callersFunctionpool_alloc
samtools-1.3/htslib-1.3/cram/pooled_alloc.c:111
↓ 9 callersFunctionsam_hdr_parse_
* Tokenises a SAM header into a hash table. * Also extracts a few bits on specific data types, such as @RG lines. * * Returns a SAM_hdr struct on s
samtools-1.3/htslib-1.3/cram/sam_header.c:931
↓ 9 callersFunctionsam_open_mode
samtools-1.3/htslib-1.3/sam.c:1317
↓ 9 callersFunctionsamtools_version
samtools-1.3/bamtk.c:65
↓ 9 callersFunctiontrans_tbl_init
samtools-1.3/bam_sort.c:784
↓ 8 callersFunctionRansDecInit
Initializes a rANS decoder. Unlike the encoder, the decoder works forwards as you'd expect.
samtools-1.3/htslib-1.3/cram/rANS_byte.h:118
↓ 8 callersFunctionRansDecRenorm
Renormalize.
samtools-1.3/htslib-1.3/cram/rANS_byte.h:322
↓ 8 callersFunctionRansEncFlush
Flushes the rANS encoder.
samtools-1.3/htslib-1.3/cram/rANS_byte.h:102
↓ 8 callersFunctionRansEncInit
Initialize a rANS encoder.
samtools-1.3/htslib-1.3/cram/rANS_byte.h:65
↓ 8 callersFunctionbam_translate
samtools-1.3/bam_sort.c:975
↓ 8 callersFunctionbcf_enc_int1
samtools-1.3/htslib-1.3/htslib/vcf.h:853
↓ 8 callersFunctionbcf_hdr_add_sample
samtools-1.3/htslib-1.3/vcf.c:59
↓ 8 callersFunctionbcf_hdr_get_hrec
* Note that while querying of FLT,INFO,FMT,CTG lines is fast (the keys are hashed), * the STR,GEN lines are searched for linearly in a linked list
samtools-1.3/htslib-1.3/vcf.c:534
↓ 8 callersMethodbegin
0-copy access :
boost/format/alt_sstream.hpp:154
↓ 8 callersFunctionbeta_small_b_large_a_series
boost/math/special_functions/beta.hpp:736
↓ 8 callersFunctionbgzf_flush
samtools-1.3/htslib-1.3/bgzf.c:737
↓ 8 callersFunctionbgzf_read_block
samtools-1.3/htslib-1.3/bgzf.c:421
↓ 8 callersFunctioncalcCI
calcCI.cpp:218
↓ 8 callersFunctioncbrt
boost/math/special_functions/cbrt.hpp:160
↓ 8 callersFunctioncheck_bam_aux_get
samtools-1.3/htslib-1.3/test/sam.c:50
↓ 8 callersFunctioncram_compress_by_method
samtools-1.3/htslib-1.3/cram/cram_io.c:1172
↓ 8 callersFunctioncram_fd_get_fp
samtools-1.3/htslib-1.3/cram/cram_external.c:59
↓ 8 callersFunctioncram_ref_decr
samtools-1.3/htslib-1.3/cram/cram_io.c:2400
↓ 8 callersFunctioncram_uncompress_block
* Uncompresses a CRAM block, if compressed. */
samtools-1.3/htslib-1.3/cram/cram_io.c:1078
↓ 8 callersFunctioncram_write_container
* Writes a container structure. * * Returns 0 on success * -1 on failure */
samtools-1.3/htslib-1.3/cram/cram_io.c:3090
↓ 8 callersMethodgetMask
RefSeq.h:89
↓ 8 callersMethodgetN
HitContainer.h:43
↓ 8 callersMethodgetSAt
HitContainer.h:50
↓ 8 callersMethodgetm
GroupInfo.h:15
↓ 8 callersFunctiongettimeofday
vxWorks claims to implement gettimeofday in sys/time.h but nevertheless does not provide it! See https://support.windriver.com/olsPortal/faces/mainten
boost/config/platform/vxworks.hpp:293
↓ 8 callersFunctionhts_md5_final
samtools-1.3/htslib-1.3/md5.c:269
↓ 8 callersFunctionhts_md5_init
samtools-1.3/htslib-1.3/md5.c:321
↓ 8 callersFunctionhts_md5_update
samtools-1.3/htslib-1.3/md5.c:235
↓ 8 callersFunctionhts_opt_add
* Parses arg and appends it to the option list. * * Returns 0 on success; * -1 on failure. */
samtools-1.3/htslib-1.3/hts.c:428
↓ 8 callersFunctionhts_set_fai_filename
samtools-1.3/htslib-1.3/hts.c:906
↓ 8 callersFunctionhts_set_threads
samtools-1.3/htslib-1.3/hts.c:896
↓ 8 callersFunctionkf_lgamma
Log gamma function * \log{\Gamma(z)} * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245 */
samtools-1.3/htslib-1.3/kfunc.c:35
↓ 8 callersFunctionkhash_str2int_get
* Returns 0 on success and -1 when the key is not present. On success, * *value is set, unless NULL is passed. */
samtools-1.3/htslib-1.3/htslib/khash_str2int.h:78
↓ 8 callersFunctionkstrtok
samtools-1.3/htslib-1.3/kstring.c:62
↓ 8 callersMethodmean
boost/math/distributions/normal.hpp:44
↓ 8 callersMethodpop_back
pop_back() - added to model the BidirectionalRangePrimitiveConcept
boost/range/iterator_range_core.hpp:335
↓ 8 callersFunctionprint_error
samtools-1.3/bamtk.c:81
↓ 8 callersFunctionraise_rounding_error
boost/math/policies/error_handling.hpp:400
↓ 8 callersFunctionsam_itr_queryi
samtools-1.3/htslib-1.3/sam.c:661
↓ 8 callersMethodseed
* Seeds an @c additive_combine_engine using the default * seeds of the two base generators. */
boost/random/additive_combine.hpp:128
↓ 8 callersFunctionshl_char_array
boost/lexical_cast.hpp:1588
↓ 8 callersFunctionstring_ndup
samtools-1.3/htslib-1.3/cram/string_alloc.c:146
↓ 8 callersFunctiontgamma_delta_ratio
boost/math/special_functions/gamma.hpp:1623
↓ 7 callersMethodGetFilename
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamReader.cpp:62
↓ 7 callersMethodGetFilename
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamReader.cpp:62
↓ 7 callersFunctionRansDecAdvanceSymbol
Equivalent to RansDecAdvance that takes a symbol.
samtools-1.3/htslib-1.3/cram/rANS_byte.h:298
↓ 7 callersFunctionRansDecGet
Returns the current cumulative frequency (map it to a symbol yourself!)
samtools-1.3/htslib-1.3/cram/rANS_byte.h:134
↓ 7 callersMethodTell
get file position in BGZF file
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BGZF.cpp:365
↓ 7 callersMethodTell
get file position in BGZF file
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BGZF.cpp:365
↓ 7 callersFunctionaddressof
boost/utility/addressof.hpp:51
↓ 7 callersFunctionbam_cigar2rlen
samtools-1.3/htslib-1.3/sam.c:327
↓ 7 callersFunctionbam_hdr_dup
samtools-1.3/htslib-1.3/sam.c:69
↓ 7 callersFunctionbcf_enc_vchar
samtools-1.3/htslib-1.3/vcf.c:1461
↓ 7 callersFunctionbcf_float_is_vector_end
samtools-1.3/htslib-1.3/htslib/vcf.h:796
↓ 7 callersFunctionbcf_hdr_init
samtools-1.3/htslib-1.3/vcf.c:750
↓ 7 callersFunctionbed_overlap
samtools-1.3/bedidx.c:118
↓ 7 callersFunctionbessel_j0
boost/math/special_functions/detail/bessel_j0.hpp:53
↓ 7 callersFunctionchecked_delete
boost/checked_delete.hpp:29
↓ 7 callersMethodcompare
bc_aux.h:18
↓ 7 callersFunctionconvert
EBSeq/calcClusteringInfo.cpp:51
↓ 7 callersFunctioncram_codec_to_id
* Returns the content_id used by this codec, also in id2 if byte_array_len. * Returns -1 for the CORE block and -2 for unneeded. * id2 is only fille
samtools-1.3/htslib-1.3/cram/cram_codecs.c:1806
↓ 7 callersFunctioncram_set_option
* Sets options on the cram_fd. See CRAM_OPT_* definitions in cram_structs.h. * Use this immediately after opening. * * Returns 0 on success *
samtools-1.3/htslib-1.3/cram/cram_io.c:4390
↓ 7 callersFunctioncyl_neumann
boost/math/special_functions/bessel.hpp:623
↓ 7 callersFunctionellint_rf_imp
boost/math/special_functions/ellint_rf.hpp:31
↓ 7 callersFunctionequal
boost/range/iterator_range_core.hpp:98
↓ 7 callersFunctionfinish_merged_header
samtools-1.3/bam_sort.c:866
↓ 7 callersFunctionfree_merged_header
samtools-1.3/bam_sort.c:936
↓ 7 callersFunctionhfile_destroy
samtools-1.3/htslib-1.3/hfile.c:101
↓ 7 callersFunctionhflush
samtools-1.3/htslib-1.3/hfile.c:212
↓ 7 callersFunctionhpeek
samtools-1.3/htslib-1.3/hfile.c:147
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