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Functions5,402 in github.com/deweylab/RSEM

⨍ Functions 5,402◇ Types & classes 14,945
↓ 2 callersFunctionmd5_one
samtools-1.3/misc/md5sum-lite.c:30
↓ 2 callersFunctionmd5_one
samtools-1.3/misc/md5fa.c:32
↓ 2 callersFunctionmd5_print
samtools-1.3/htslib-1.3/cram/cram_decode.c:2104
↓ 2 callersMethodmean
Returns the mean of the distribution. */
boost/random/normal_distribution.hpp:116
↓ 2 callersMethodmean
Returns the "mean" parameter of the distribution. */
boost/random/poisson_distribution.hpp:169
↓ 2 callersMethodmedian
Returns: the "median" parameter of the distribution */
boost/random/cauchy_distribution.hpp:115
↓ 2 callersFunctionmfload
* Reads the entirety of fp into memory. If 'fn' exists it is the filename * associated with fp. This will be used for more optimal reading (via a *
samtools-1.3/htslib-1.3/cram/mFILE.c:74
↓ 2 callersFunctionmfreopen
* Converts a FILE * to an mFILE *. * Use this for wrapper functions to turn external prototypes requring * FILE * as an argument into internal code
samtools-1.3/htslib-1.3/cram/mFILE.c:255
↓ 2 callersMethodmodulus
boost/random/lagged_fibonacci.hpp:393
↓ 2 callersFunctionmp_alloc
samtools-1.3/bam_lpileup.c:58
↓ 2 callersFunctionmpileup
* Performs pileup * @param conf configuration for this pileup * @param n number of files specified in fn * @param fn filenames */
samtools-1.3/bam_plcmd.c:304
↓ 2 callersFunctionmplp_get_ref
samtools-1.3/bam_plcmd.c:153
↓ 2 callersFunctionmt_flush_queue
samtools-1.3/htslib-1.3/bgzf.c:689
↓ 2 callersFunctionmt_queue
samtools-1.3/htslib-1.3/bgzf.c:679
↓ 2 callersFunctionmuldivmod
boost/random/detail/large_arithmetic.hpp:32
↓ 2 callersFunctionmy_netread
samtools-1.3/htslib-1.3/knetfile.c:182
↓ 2 callersMethodn
Returns the @c n parameter of the distribution. */
boost/random/chi_squared_distribution.hpp:127
↓ 2 callersMethodn
Returns the number of degrees of freedom. */
boost/random/student_t_distribution.hpp:113
↓ 2 callersFunctionnew_tag
name points to "XY", value_from points to the first character of the value string and value_to points to the last character of the value string.
samtools-1.3/sam_header.c:207
↓ 2 callersFunctionnext
boost/next_prior.hpp:30
↓ 2 callersFunctionopen_nextdir
samtools-1.3/htslib-1.3/plugin.c:50
↓ 2 callersFunctionoutput
getUnique.cpp:25
↓ 2 callersFunctionoutput_stats
samtools-1.3/stats.c:991
↓ 2 callersFunctionowens_t
boost/math/special_functions/owens_t.hpp:953
↓ 2 callersFunctionowens_t_T1_accelerated
boost/math/special_functions/owens_t.hpp:537
↓ 2 callersFunctionowens_t_T2_accelerated
boost/math/special_functions/owens_t.hpp:653
↓ 2 callersMethodp
Returns the @c p parameter of the distribution. */
boost/random/negative_binomial_distribution.hpp:137
↓ 2 callersMethodp
Returns the @c p parameter of the distribution. */
boost/random/binomial_distribution.hpp:180
↓ 2 callersMethodp
* Returns: The "p" parameter of the distribution. */
boost/random/bernoulli_distribution.hpp:113
↓ 2 callersFunctionpackInt32
samtools-1.3/htslib-1.3/bgzf.c:103
↓ 2 callersMethodparam
Returns the parameters of the distribution. */
boost/random/discrete_distribution.hpp:330
↓ 2 callersMethodparam
Returns the parameters of the distribution. */
boost/random/weibull_distribution.hpp:125
↓ 2 callersMethodparam
Returns the parameters of the distribution. */
boost/random/uniform_real_distribution.hpp:174
↓ 2 callersMethodparam
Returns the parameters of the distribution. */
boost/random/fisher_f_distribution.hpp:128
↓ 2 callersMethodparam
Returns the parameters of the distribution. */
boost/random/extreme_value_distribution.hpp:125
↓ 2 callersMethodparam
Returns the parameters of the distribution. */
boost/random/student_t_distribution.hpp:123
↓ 2 callersMethodparam
Returns the parameters of the distribution. */
boost/random/uniform_int_distribution.hpp:335
↓ 2 callersMethodparam
Returns the parameters of the distribution. */
boost/random/geometric_distribution.hpp:134
↓ 2 callersMethodparam
Returns the parameters of the distribution. */
boost/random/triangle_distribution.hpp:140
↓ 2 callersMethodparse
GTFItem.h:51
↓ 2 callersFunctionparse_inf_nan
boost/lexical_cast.hpp:1096
↓ 2 callersFunctionparse_ini
samtools-1.3/htslib-1.3/hfile_libcurl.c:716
↓ 2 callersFunctionparse_version
Parse "x.y" text, taking care because the string is not NUL-terminated and filling in major/minor only when the digits are followed by a delimiter, so
samtools-1.3/htslib-1.3/hts.c:156
↓ 2 callersFunctionpolishTheta
WriteResults.h:55
↓ 2 callersMethodpoolTagAlign
(self)
pRSEM/ChIPSeqExperiment.py:116
↓ 2 callersFunctionpool_free
samtools-1.3/htslib-1.3/cram/pooled_alloc.c:140
↓ 2 callersFunctionpowm1_imp
boost/math/special_functions/powm1.hpp:21
↓ 2 callersFunctionprintUsage
bam2wig.cpp:9
↓ 2 callersFunctionprint_header_line
samtools-1.3/sam_header.c:478
↓ 2 callersFunctionprint_usage
samtools-1.3/bam_plcmd.c:769
↓ 2 callersFunctionprintw
samtools-1.3/bam_plcmd.c:44
↓ 2 callersFunctionprior
boost/fusion/iterator/prior.hpp:56
↓ 2 callersFunctionprocess_aln
Returns 0 to indicate read should be output 1 otherwise
samtools-1.3/sam_view.c:71
↓ 2 callersFunctionprocess_cns
samtools-1.3/cut_target.c:92
↓ 2 callersFunctionput_head
boost/format/feed_args.hpp:78
↓ 2 callersMethodquicklyConstructFromRSEMTI
quickly construct Transcript from the 6 lines from RSEM .TI file, the last line won't be parsed.
pRSEM/Transcript.py:66
↓ 2 callersMethodrandom
simul.h:37
↓ 2 callersFunctionrange_begin
boost/range/begin.hpp:57
↓ 2 callersFunctionrange_end
boost/range/end.hpp:58
↓ 2 callersFunctionrans_compress_O0
samtools-1.3/htslib-1.3/cram/rANS_static.c:69
↓ 2 callersFunctionrans_uncompress
samtools-1.3/htslib-1.3/cram/rANS_static.c:746
↓ 2 callersMethodrbegin
boost/array.hpp:104
↓ 2 callersFunctionread_file_list
samtools-1.3/bam_plcmd.c:683
↓ 2 callersFunctionrealloc_buffers
samtools-1.3/stats.c:549
↓ 2 callersFunctionrealloc_gcd_buffer
samtools-1.3/stats.c:543
↓ 2 callersFunctionrefs_load_fai
* Loads a FAI file for a reference.fasta. * "is_err" indicates whether failure to load is worthy of emitting an * error message. In some cases (eg w
samtools-1.3/htslib-1.3/cram/cram_io.c:1794
↓ 2 callersFunctionrelease
EM.cpp:288
↓ 2 callersFunctionremove_pads
remove pads
samtools-1.3/misc/ace2sam.c:54
↓ 2 callersMethodrend
boost/array.hpp:112
↓ 2 callersFunctionreplace_cigar
samtools-1.3/padding.c:42
↓ 2 callersMethodreset
ReadReader.h:112
↓ 2 callersMethodreset
boost/random/uniform_01.hpp:89
↓ 2 callersFunctionrising_factorial_imp
boost/math/special_functions/factorials.hpp:117
↓ 2 callersFunctionrmdup_usage
samtools-1.3/bam_rmdup.c:206
↓ 2 callersFunctionrtrans_build
samtools-1.3/bam_sort.c:1042
↓ 2 callersMethods
Returns the s parameter of the distribution. */
boost/random/lognormal_distribution.hpp:114
↓ 2 callersFunctionsam_hdr_PG_ID
* Returns a unique ID from a base name. * * The value returned is valid until the next call to * this function. */
samtools-1.3/htslib-1.3/cram/sam_header.c:1161
↓ 2 callersFunctionsam_hdr_rebuild
* Reconstructs the kstring from the header hash table. * Returns 0 on success * -1 on failure */
samtools-1.3/htslib-1.3/cram/sam_header.c:793
↓ 2 callersFunctionsam_hdr_sort_order
* Returns the sort order: */
samtools-1.3/htslib-1.3/cram/sam_header.c:756
↓ 2 callersFunctionsam_hdr_update
* Adds or updates tag key,value pairs in a header line. * Eg for adding M5 tags to @SQ lines or updating sort order for the * @HD line (although use
samtools-1.3/htslib-1.3/cram/sam_header.c:709
↓ 2 callersFunctionsam_hdr_update_hashes
Updates the hash tables in the SAM_hdr structure. * * Returns 0 on success; * -1 on failure */
samtools-1.3/htslib-1.3/cram/sam_header.c:97
↓ 2 callersFunctionsam_header_line_clone
samtools-1.3/sam_header.c:313
↓ 2 callersFunctionsam_header_line_free
samtools-1.3/sam_header.c:499
↓ 2 callersFunctionsamfaipath
samtools-1.3/sam.c:115
↓ 2 callersFunctionsamread
! @abstract Read one alignment @param fp file handler @param b alignment @return bytes read */
samtools-1.3/sam.h:95
↓ 2 callersFunctionsanitise_SQ_lines
* Verifies that the CRAM @SQ lines and .fai files match. */
samtools-1.3/htslib-1.3/cram/cram_io.c:1935
↓ 2 callersMethodseed
Seeds the generator with the default seed. */
boost/random/linear_congruential.hpp:384
↓ 2 callersMethodsetAsNormal
Please give interger mean, thanks! minL: new minimum length, maxL: new maximum length
LenDist.h:113
↓ 2 callersFunctionshr_using_base_class
boost/lexical_cast.hpp:1982
↓ 2 callersFunctionshrink_hash
samtools-1.3/phase.c:470
↓ 2 callersMethodsigma
Returns the standard deviation of the distribution. */
boost/random/normal_distribution.hpp:118
↓ 2 callersMethodsigma
Returns: the "sigma" parameter of the distribution */
boost/random/cauchy_distribution.hpp:117
↓ 2 callersFunctionsinc_pi_imp
boost/math/special_functions/sinc.hpp:42
↓ 2 callersFunctionskip_asterisk
boost/format/parsing.hpp:90
↓ 2 callersFunctionskip_aux
samtools-1.3/htslib-1.3/sam.c:1233
↓ 2 callersFunctionslurp
samtools-1.3/htslib-1.3/test/hfile.c:58
↓ 2 callersFunctionsort_blocks
samtools-1.3/bam_sort.c:1590
↓ 2 callersFunctionsp_enable_shared_from_this
boost/smart_ptr/shared_ptr.hpp:208
↓ 2 callersFunctionstandard_deviation
boost/math/distributions/detail/derived_accessors.hpp:45
↓ 2 callersFunctionstats_init
samtools-1.3/stats.c:1494
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