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Functions5,402 in github.com/deweylab/RSEM

⨍ Functions 5,402◇ Types & classes 14,945
↓ 5 callersFunctionbessel_j1
boost/math/special_functions/detail/bessel_j1.hpp:53
↓ 5 callersFunctionbgzf_index_dump
samtools-1.3/htslib-1.3/bgzf.c:969
↓ 5 callersFunctioncleanup_opts
samtools-1.3/bam_addrprg.c:64
↓ 5 callersFunctioncos_pi
boost/math/special_functions/cos_pi.hpp:53
↓ 5 callersFunctioncram_container_get_length
*----------------------------------------------------------------------------- * cram_container */
samtools-1.3/htslib-1.3/cram/cram_external.c:67
↓ 5 callersFunctioncram_stats_del
samtools-1.3/htslib-1.3/cram/cram_stats.c:76
↓ 5 callersFunctionellint_k_imp
boost/math/special_functions/ellint_1.hpp:121
↓ 5 callersFunctionempty
boost/range/empty.hpp:26
↓ 5 callersFunctionexpint_imp
boost/math/special_functions/expint.hpp:433
↓ 5 callersFunctionfai_build
samtools-1.3/htslib-1.3/faidx.c:210
↓ 5 callersMethodfill
boost/format/detail/workarounds_gcc-2_95.hpp:73
↓ 5 callersFunctiongamma_incomplete_imp
boost/math/special_functions/gamma.hpp:823
↓ 5 callersFunctiongcd_percentile
samtools-1.3/stats.c:975
↓ 5 callersFunctiongenerate
boost/random/detail/seed_impl.hpp:219
↓ 5 callersFunctiongetCharacter
utils.h:96
↓ 5 callersMethodgetStrand
GTFItem.h:130
↓ 5 callersFunctionhalley_iterate
boost/math/tools/roots.hpp:272
↓ 5 callersMethodhasPolyA
Refs.h:40
↓ 5 callersFunctionhts_format_file_extension
samtools-1.3/htslib-1.3/hts.c:855
↓ 5 callersFunctionhts_opt_apply
* Applies an hts_opt option list to a given htsFile. * * Returns 0 on success * -1 on failure */
samtools-1.3/htslib-1.3/hts.c:536
↓ 5 callersFunctionhypergeo_acc
incremental version of hypergenometric distribution
samtools-1.3/htslib-1.3/kfunc.c:216
↓ 5 callersFunctionibeta_a_step
boost/math/special_functions/beta.hpp:648
↓ 5 callersFunctioninteger_log2
boost/random/detail/integer_log2.hpp:71
↓ 5 callersFunctionis_nan_helper
boost/math/special_functions/fpclassify.hpp:103
↓ 5 callersFunctionitf8_get
* As above, but decoding from memory */
samtools-1.3/htslib-1.3/cram/cram_io.c:251
↓ 5 callersFunctionkget_int32
samtools-1.3/htslib-1.3/cram/cram_index.c:88
↓ 5 callersFunctionkhash_str2int_destroy
* Destroy the hash structure, but not the keys */
samtools-1.3/htslib-1.3/htslib/khash_str2int.h:44
↓ 5 callersFunctionknet_read
samtools-1.3/htslib-1.3/knetfile.c:514
↓ 5 callersFunctionlist_append
samtools-1.3/sam_header.c:114
↓ 5 callersFunctionlog1pmx
boost/math/special_functions/log1p.hpp:457
↓ 5 callersFunctionmove_kstr_to_text
samtools-1.3/bam_sort.c:855
↓ 5 callersFunctionmp_free
samtools-1.3/bam_lpileup.c:64
↓ 5 callersFunctionmulti_errno
samtools-1.3/htslib-1.3/hfile_libcurl.c:161
↓ 5 callersFunctionoverlap_remove
samtools-1.3/htslib-1.3/sam.c:1829
↓ 5 callersFunctionprint_vector
boost/random/detail/vector_io.hpp:25
↓ 5 callersFunctionread_vector
boost/random/detail/vector_io.hpp:44
↓ 5 callersFunctionrefs_free
samtools-1.3/htslib-1.3/cram/cram_io.c:1683
↓ 5 callersMethodrelease
boost/smart_ptr/detail/sp_counted_base_nt.hpp:76
↓ 5 callersFunctionreopen
samtools-1.3/htslib-1.3/test/hfile.c:81
↓ 5 callersFunctionsam_hdr_error
samtools-1.3/htslib-1.3/cram/sam_header.c:39
↓ 5 callersFunctionsam_hdr_find_key
* Looks for a specific key in a single sam header line. * If prev is non-NULL it also fills this out with the previous tag, to * permit use in key r
samtools-1.3/htslib-1.3/cram/sam_header.c:677
↓ 5 callersMethodsetConPrb
SingleHit.h:32
↓ 5 callersFunctionstr_end
boost/range/detail/implementation_help.hpp:35
↓ 5 callersFunctionstring_dup
samtools-1.3/htslib-1.3/cram/string_alloc.c:142
↓ 5 callersFunctionstring_pool_destroy
samtools-1.3/htslib-1.3/cram/string_alloc.c:96
↓ 5 callersMethodswap
swap (note: linear complexity)
boost/array.hpp:165
↓ 5 callersFunctiont_pool_delete_result
* Frees a result 'r' and if free_data is true also frees * the internal r->data result too. */
samtools-1.3/htslib-1.3/cram/thread_pool.c:243
↓ 5 callersFunctiontag_exists
Look for a tag "XY" in a predefined const char *[] array.
samtools-1.3/sam_header.c:148
↓ 5 callersFunctiontbx_index_load
samtools-1.3/htslib-1.3/tbx.c:304
↓ 5 callersFunctiontbx_seqnames
samtools-1.3/htslib-1.3/tbx.c:309
↓ 5 callersFunctiontgamma1pm1
boost/math/special_functions/gamma.hpp:1483
↓ 5 callersMethodunlock
boost/smart_ptr/detail/spinlock_pt.hpp:44
↓ 5 callersFunctionwait_perform
samtools-1.3/htslib-1.3/hfile_libcurl.c:221
↓ 5 callersFunctionwhich_readpart
samtools-1.3/sam_view.c:655
↓ 5 callersFunctionwrap_isdigit
boost/format/parsing.hpp:46
↓ 4 callersMethodGetReferenceData
returns vector of reference objects
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamMultiReader.cpp:250
↓ 4 callersMethodGetReferenceData
returns vector of reference objects
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamMultiReader.cpp:250
↓ 4 callersMethodRewind
rewind index file to beginning of index data, return true if rewound OK
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamIndex.cpp:148
↓ 4 callersMethodRewind
rewind index file to beginning of index data, return true if rewound OK
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamIndex.cpp:148
↓ 4 callersMethodSetCacheMode
change the index caching behavior
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamIndex.cpp:153
↓ 4 callersMethodSetCacheMode
change the index caching behavior
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamIndex.cpp:153
↓ 4 callersFunctionSwapEndian_32p
swaps endianness of 'next 4 bytes' in a char buffer (in-place)
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamAux.h:208
↓ 4 callersFunctionSwapEndian_32p
swaps endianness of 'next 4 bytes' in a char buffer (in-place)
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamAux.h:208
↓ 4 callersFunctionSystemIsBigEndian
returns true if system is big endian
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.3/src/BamAux.h:145
↓ 4 callersFunctionSystemIsBigEndian
returns true if system is big endian
pRSEM/phantompeakqualtools/spp_1.10.1_on_R3.2/src/BamAux.h:145
↓ 4 callersMethoda
Returns the minimum value of the distribution. */
boost/random/uniform_smallint.hpp:168
↓ 4 callersFunctionadd_header
samtools-1.3/htslib-1.3/hfile_libcurl.c:449
↓ 4 callersFunctionadd_pair
samtools-1.3/sample.c:56
↓ 4 callersFunctionassign_value
boost/optional/optional.hpp:433
↓ 4 callersFunctionasymptotic_bessel_large_x_limit
boost/math/special_functions/detail/bessel_jy_asym.hpp:123
↓ 4 callersMethodb
Returns the maximum value of the distribution. */
boost/random/uniform_smallint.hpp:170
↓ 4 callersFunctionbam_aux_type2size
sam_utils.h:25
↓ 4 callersFunctionbam_is_unmapped
sam_utils.h:50
↓ 4 callersFunctionbam_plp_destroy
samtools-1.3/htslib-1.3/sam.c:1636
↓ 4 callersFunctionbam_plp_init
samtools-1.3/htslib-1.3/sam.c:1614
↓ 4 callersFunctionbam_plp_next
Prepares next pileup position in bam records collected by bam_plp_auto -> user func -> bam_plp_push. Returns pointer to the piled records if next posi
samtools-1.3/htslib-1.3/sam.c:1853
↓ 4 callersFunctionbam_prob_realn_core
samtools-1.3/bam_md.c:212
↓ 4 callersFunctionbcf_dec_size
samtools-1.3/htslib-1.3/htslib/vcf.h:894
↓ 4 callersFunctionbcf_get_variant_types
samtools-1.3/htslib-1.3/vcf.c:2772
↓ 4 callersFunctionbcf_hdr_name2id
* bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID * bcf_hdr_id2name() - Translates numeric ID to sequence name
samtools-1.3/htslib-1.3/htslib/vcf.h:703
↓ 4 callersFunctionbcf_unpack_info_core1
samtools-1.3/htslib-1.3/vcf.c:1980
↓ 4 callersFunctionbcf_update_format
samtools-1.3/htslib-1.3/vcf.c:2896
↓ 4 callersFunctionbed_destroy
samtools-1.3/bedidx.c:246
↓ 4 callersFunctionbessel_j_small_z_series
boost/math/special_functions/detail/bessel_jy_series.hpp:47
↓ 4 callersFunctionbessel_jy
boost/math/special_functions/detail/bessel_jy.hpp:265
↓ 4 callersFunctionbgzf_index_build_init
samtools-1.3/htslib-1.3/bgzf.c:945
↓ 4 callersFunctionbody
* This processes one or more 64-byte data blocks, but does NOT update * the bit counters. There are no alignment requirements. */
samtools-1.3/htslib-1.3/md5.c:117
↓ 4 callersMethodcalcInitParams
NoiseProfile.h:91
↓ 4 callersFunctioncalc_mwu_bias
samtools-1.3/bam2bcf.c:413
↓ 4 callersFunctioncalc_mwu_bias_cdf
samtools-1.3/bam2bcf.c:369
↓ 4 callersMethodcall
boost/random/detail/seed_impl.hpp:55
↓ 4 callersFunctioncheck_sam_close
samtools-1.3/sam_view.c:217
↓ 4 callersFunctioncheck_sam_write1
samtools-1.3/sam_view.c:205
↓ 4 callersFunctioncollect_stats
samtools-1.3/stats.c:757
↓ 4 callersFunctioncomplement
boost/math/distributions/complement.hpp:156
↓ 4 callersFunctioncram_block_size
* Computes the size of a cram block, including the block * header itself. */
samtools-1.3/htslib-1.3/cram/cram_io.c:1002
↓ 4 callersFunctioncram_decode_compression_header
* Decodes a CRAM block compression header. * Returns header ptr on success * NULL on failure */
samtools-1.3/htslib-1.3/cram/cram_decode.c:129
↓ 4 callersFunctioncram_ref_incr_locked
samtools-1.3/htslib-1.3/cram/cram_io.c:2359
↓ 4 callersFunctioncram_seek
* Seek within a CRAM file. * * Returns 0 on success * -1 on failure */
samtools-1.3/htslib-1.3/cram/cram_io.c:4228
↓ 4 callersFunctioncyl_bessel_i
boost/math/special_functions/bessel.hpp:580
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