MCPcopy Create free account

hub / github.com/deweylab/RSEM / functions

Functions5,402 in github.com/deweylab/RSEM

⨍ Functions 5,402◇ Types & classes 14,945
↓ 4 callersFunctioned_swap_8
samtools-1.3/htslib-1.3/htslib/hts.h:621
↓ 4 callersFunctionellint_f_imp
boost/math/special_functions/ellint_1.hpp:42
↓ 4 callersFunctionerror
samtools-1.3/faidx.c:35
↓ 4 callersFunctionevaluate_polynomial_c_imp
boost/math/tools/rational.hpp:176
↓ 4 callersFunctionfatal
a fatal error
samtools-1.3/misc/ace2sam.c:48
↓ 4 callersFunctionflush_buffer
Flushes the write buffer, fp->[buffer,begin), out through the backend returning 0 on success or negative if an error occurred. */
samtools-1.3/htslib-1.3/hfile.c:198
↓ 4 callersMethodfront
convenience
boost/range/iterator_range_core.hpp:314
↓ 4 callersMethodget
boost/fusion/sequence/io/detail/manip.hpp:75
↓ 4 callersMethodgetLength
Transcript.h:71
↓ 4 callersMethodgetNextHit
HitWrapper.h:18
↓ 4 callersMethodgetSeq
RefSeq.h:71
↓ 4 callersFunctionget_object
This workaround is supposed to silence GCC warnings about broken strict aliasing rules
boost/optional/optional.hpp:455
↓ 4 callersFunctionget_ptr_impl
boost/optional/optional.hpp:447
↓ 4 callersFunctiongreater_or_equal_than
boost/range/iterator_range_core.hpp:90
↓ 4 callersFunctiongreater_than
boost/range/iterator_range_core.hpp:78
↓ 4 callersFunctionhash_rg
samtools-1.3/bam_cat.c:120
↓ 4 callersFunctionhdopen
samtools-1.3/htslib-1.3/hfile.c:447
↓ 4 callersFunctionhputc
! @abstract Write a character to the stream @return The character written, or EOF if an error occurred. */
samtools-1.3/htslib-1.3/htslib/hfile.h:165
↓ 4 callersFunctionhts_hopen
samtools-1.3/htslib-1.3/hts.c:678
↓ 4 callersFunctionhts_idx_load2
samtools-1.3/htslib-1.3/hts.c:2044
↓ 4 callersFunctionhts_idx_save_as
samtools-1.3/htslib-1.3/hts.c:1480
↓ 4 callersFunctionhts_reg2bin
samtools-1.3/htslib-1.3/htslib/hts.h:578
↓ 4 callersFunctionibeta_inv_ab_imp
boost/math/special_functions/detail/ibeta_inv_ab.hpp:74
↓ 4 callersMethodinit
RSPD.h:110
↓ 4 callersMethodinitFromParam
(cls, param, is_control, param_attr)
pRSEM/ChIPSeqExperiment.py:27
↓ 4 callersFunctioninit_add_plugin
samtools-1.3/htslib-1.3/hfile.c:618
↓ 4 callersFunctionint32_decode
* Decodes a 32-bit little endian value from fd and stores in val. * * Returns the number of bytes read on success * -1 on failure */
samtools-1.3/htslib-1.3/cram/cram_io.c:641
↓ 4 callersFunctionis_initialized
boost/optional/optional.hpp:340
↓ 4 callersFunctionkftp_get_response
samtools-1.3/htslib-1.3/knetfile.c:204
↓ 4 callersFunctionkhash_str2int_inc
* Add a new string to the dictionary, auto-incrementing the value. * On success returns the newly inserted integer id, on error -1 * is returned.
samtools-1.3/htslib-1.3/htslib/khash_str2int.h:96
↓ 4 callersFunctionknet_close
samtools-1.3/htslib-1.3/knetfile.c:576
↓ 4 callersFunctionkpa_glocal
The topology of the profile HMM: /\ /\ /\ /\ I[1] I[k-1] I[k] I[L]
samtools-1.3/kprobaln.c:72
↓ 4 callersFunctionlanczos_sum
boost/math/special_functions/lanczos.hpp:739
↓ 4 callersFunctionless_equal
boost/fusion/sequence/comparison/less_equal.hpp:26
↓ 4 callersFunctionless_or_equal_than
boost/range/iterator_range_core.hpp:84
↓ 4 callersMethodloadRefs
inpF in fasta format, with sequence all in one line together option 0 read all, 1 do not read sequences
Refs.h:118
↓ 4 callersFunctionload_unpadded_ref
samtools-1.3/padding.c:107
↓ 4 callersMethodlock
boost/smart_ptr/detail/spinlock_pt.hpp:39
↓ 4 callersFunctionmatch_to_ks
Append a header line match to kstring
samtools-1.3/bam_sort.c:302
↓ 4 callersFunctionmerge_usage
samtools-1.3/bam_sort.c:1366
↓ 4 callersFunctionmfdestroy
* Destroys an mFILE structure but does not flush or close it */
samtools-1.3/htslib-1.3/cram/mFILE.c:395
↓ 4 callersFunctionmp_free
samtools-1.3/htslib-1.3/sam.c:1497
↓ 4 callersFunctionnbits
Returns the number of bits set in val; it the highest bit used */
samtools-1.3/htslib-1.3/cram/cram_stats.c:121
↓ 4 callersFunctionok
Added for RSEM by Bo Li: Test if the query name should stop
samtools-1.3/bam_sort.c:72
↓ 4 callersMethodparam
Returns the parameters of the distribution. */
boost/random/piecewise_constant_distribution.hpp:404
↓ 4 callersFunctionparse_inf_nan_impl
boost/lexical_cast.hpp:1003
↓ 4 callersMethodpbase
boost/lexical_cast.hpp:1448
↓ 4 callersFunctionpool_destroy
samtools-1.3/htslib-1.3/cram/pooled_alloc.c:101
↓ 4 callersFunctionpowm1
boost/math/special_functions/powm1.hpp:38
↓ 4 callersMethodprocess
wiggle.cpp:97
↓ 4 callersFunctionput_inf_nan_impl
boost/lexical_cast.hpp:1060
↓ 4 callersFunctionquadratic_interpolate
boost/math/tools/toms748_solve.hpp:178
↓ 4 callersFunctionrange_to_ks
Append char range to kstring
samtools-1.3/bam_sort.c:296
↓ 4 callersMethodreadFrom
Transcripts.h:81
↓ 4 callersFunctionrefs_from_header
* Generates refs_t entries based on @SQ lines in the header. * Returns 0 on success * -1 on failure */
samtools-1.3/htslib-1.3/cram/cram_io.c:2011
↓ 4 callersFunctionregidx_destroy
samtools-1.3/htslib-1.3/regidx.c:221
↓ 4 callersFunctionsafe_div
boost/math/tools/toms748_solve.hpp:140
↓ 4 callersFunctionsam_global_args_init
samtools-1.3/sam_opts.c:137
↓ 4 callersFunctionsam_hdr_add_PG
* Add an @PG line. * * If we wish complete control over this use sam_hdr_add() directly. This * function uses that, but attempts to do a lot of ted
samtools-1.3/htslib-1.3/cram/sam_header.c:1190
↓ 4 callersFunctionsam_hdr_find
* Returns the first header item matching 'type'. If ID is non-NULL it checks * for the tag ID: and compares against the specified ID. * * Returns N
samtools-1.3/htslib-1.3/cram/sam_header.c:570
↓ 4 callersFunctionsam_itr_querys
samtools-1.3/htslib-1.3/sam.c:678
↓ 4 callersMethodseed
* Seeds an @c independent_bits_engine using the default * seed of the base generator. */
boost/random/independent_bits.hpp:104
↓ 4 callersMethodseed
Calls @c seed() for both base generators. */
boost/random/xor_combine.hpp:90
↓ 4 callersMethodseed
boost/random/shuffle_order.hpp:107
↓ 4 callersMethodseed
Calls @c seed(default_seed). */
boost/random/lagged_fibonacci.hpp:84
↓ 4 callersMethodseed
default seeds the underlying generator. */
boost/random/discard_block.hpp:92
↓ 4 callersFunctionshl_char
HELPER FUNCTIONS FOR OPERATORS << ( ... ) ********************************/
boost/lexical_cast.hpp:1562
↓ 4 callersFunctionshl_char_array_limited
boost/lexical_cast.hpp:1604
↓ 4 callersFunctionshl_real_type
boost/lexical_cast.hpp:1652
↓ 4 callersFunctionsinpx
boost/math/special_functions/gamma.hpp:78
↓ 4 callersFunctionstore_bits_MSB
* Can store up to 24-bits worth of data encoded in an integer value * Possibly we'd want to have a less optimal store_bits function when dealing * w
samtools-1.3/htslib-1.3/cram/cram_codecs.c:256
↓ 4 callersFunctionstr
boost/format/free_funcs.hpp:21
↓ 4 callersFunctionstring_pool_create
samtools-1.3/htslib-1.3/cram/string_alloc.c:54
↓ 4 callersFunctiontrunc
boost/math/special_functions/trunc.hpp:20
↓ 4 callersFunctionunpackInt16
samtools-1.3/htslib-1.3/bgzf.c:98
↓ 4 callersMethodupdate
PairedEndModel.h:156
↓ 4 callersMethodupdate
SingleQModel.h:168
↓ 4 callersFunctionupdate_posmap
samtools-1.3/padding.c:174
↓ 4 callersFunctionurldecode_kput
samtools-1.3/htslib-1.3/hfile_libcurl.c:635
↓ 4 callersFunctionusage_exit
samtools-1.3/bam_stat.c:93
↓ 4 callersMethoduse_count
boost/smart_ptr/detail/shared_ptr_nmt.hpp:131
↓ 4 callersMethodweak_add_ref
boost/smart_ptr/detail/sp_counted_base_nt.hpp:85
↓ 4 callersFunctionworker_id
samtools-1.3/htslib-1.3/cram/thread_pool.c:50
↓ 3 callersFunctionCF1_jy
boost/math/special_functions/detail/bessel_jy.hpp:144
↓ 3 callersFunctionFileExists
returns whether file exists (can be opened OK)
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamAux.h:220
↓ 3 callersFunctionFileExists
returns whether file exists (can be opened OK)
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamAux.h:220
↓ 3 callersMethodGetNextAlignmentCore
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamReader.cpp:55
↓ 3 callersMethodGetNextAlignmentCore
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamReader.cpp:55
↓ 3 callersMethodGetReferenceCount
returns the number of reference sequences
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamMultiReader.cpp:245
↓ 3 callersMethodGetReferenceCount
returns the number of reference sequences
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamMultiReader.cpp:245
↓ 3 callersFunction_regions_parse_line
ichr,ifrom,ito are 0-based; returns -1 on error, 0 if the line is a comment line, 1 on success
samtools-1.3/htslib-1.3/synced_bcf_reader.c:938
↓ 3 callersMethoda
Returns the minimum value of the distribution */
boost/random/uniform_real_distribution.hpp:169
↓ 3 callersMethoda
Returns the minimum value of the distribution */
boost/random/uniform_int_distribution.hpp:330
↓ 3 callersMethodalignReadByBowtie
(self)
pRSEM/ChIPSeqExperiment.py:78
↓ 3 callersMethodalpha
Returns the "alpha" paramter of the distribution. */
boost/random/gamma_distribution.hpp:132
↓ 3 callersFunctionappend_string
boost/format/parsing.hpp:389
↓ 3 callersFunctionappend_uint32
samtools-1.3/htslib-1.3/cram/cram_io.h:309
↓ 3 callersFunctionasymptotic_bessel_y_large_x_2
boost/math/special_functions/detail/bessel_jy_asym.hpp:66
↓ 3 callersMethodb
Returns the maximum value of the distribution */
boost/random/uniform_real_distribution.hpp:171
↓ 3 callersMethodb
Returns the maximum value of the distribution */
boost/random/uniform_int_distribution.hpp:332
← previousnext →501–600 of 5,402, ranked by callers