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Functions5,402 in github.com/deweylab/RSEM

⨍ Functions 5,402◇ Types & classes 14,945
↓ 2 callersMethodadd
Transcripts.h:50
↓ 2 callersMethodadd_ref_copy
boost/smart_ptr/detail/sp_counted_base_nt.hpp:64
↓ 2 callersMethodadd_ref_lock
boost/smart_ptr/detail/sp_counted_base_nt.hpp:69
↓ 2 callersFunctionadd_to_appropriate_arr
scanForPairedEndReads.cpp:24
↓ 2 callersFunctionappend_sub32
samtools-1.3/htslib-1.3/cram/cram_io.h:347
↓ 2 callersFunctionappend_uint64
samtools-1.3/htslib-1.3/cram/cram_io.h:361
↓ 2 callersFunctionasymptotic_bessel_amplitude
boost/math/special_functions/detail/bessel_jy_asym.hpp:24
↓ 2 callersFunctionasymptotic_bessel_phase_mx
boost/math/special_functions/detail/bessel_jy_asym.hpp:42
↓ 2 callersFunctionatomic_decrement
boost/smart_ptr/detail/sp_counted_base_snc_ps3.hpp:58
↓ 2 callersFunctionatomic_decrement
boost/smart_ptr/detail/sp_counted_base_vacpp_ppc.hpp:45
↓ 2 callersFunctionatomic_decrement
boost/smart_ptr/detail/sp_counted_base_gcc_sparc.hpp:63
↓ 2 callersFunctionatomic_decrement
boost/smart_ptr/detail/sp_counted_base_acc_ia64.hpp:34
↓ 2 callersFunctionatomic_decrement
boost/smart_ptr/detail/sp_counted_base_gcc_ppc.hpp:55
↓ 2 callersFunctionatomic_decrement
boost/smart_ptr/detail/sp_counted_base_gcc_mips.hpp:52
↓ 2 callersFunctionatomic_decrement
boost/smart_ptr/detail/sp_counted_base_cw_ppc.hpp:50
↓ 2 callersFunctionatomic_decrement
boost/smart_ptr/detail/sp_counted_base_gcc_ia64.hpp:41
↓ 2 callersFunctionatomic_decrement
boost/smart_ptr/detail/sp_counted_base_sync.hpp:46
↓ 2 callersFunctionatomic_decrement
boost/smart_ptr/detail/sp_counted_base_aix.hpp:40
↓ 2 callersFunctionatomic_exchange_and_add
boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp:35
↓ 2 callersFunctionatomic_fetch_and_add
boost/smart_ptr/detail/sp_counted_base_gcc_sparc.hpp:41
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_snc_ps3.hpp:53
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_vacpp_ppc.hpp:37
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_gcc_sparc.hpp:58
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_acc_ia64.hpp:27
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_gcc_ppc.hpp:35
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_gcc_mips.hpp:31
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp:55
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_spin.hpp:39
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_cw_ppc.hpp:35
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_gcc_ia64.hpp:27
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_sync.hpp:41
↓ 2 callersFunctionatomic_increment
boost/smart_ptr/detail/sp_counted_base_aix.hpp:33
↓ 2 callersMethodb
Returns the "b" parameter of the distribution. */
boost/random/weibull_distribution.hpp:116
↓ 2 callersMethodb
Returns the "b" parameter of the distribution. */
boost/random/extreme_value_distribution.hpp:115
↓ 2 callersMethodb
Returns the @c b parameter of the distribution */
boost/random/triangle_distribution.hpp:130
↓ 2 callersFunctionbam1_to_fq
Transform a bam1_t record into a string with the FASTQ representation of it @returns false for error, true for success
samtools-1.3/sam_view.c:668
↓ 2 callersFunctionbam_aux2A
samtools-1.3/htslib-1.3/sam.c:1301
↓ 2 callersFunctionbam_aux_getCEi
! @abstract Get the color error profile at the give position @param b pointer to an alignment @return the original color if the colo
samtools-1.3/bam_color.c:122
↓ 2 callersFunctionbam_cap_mapQ
samtools-1.3/bam_md.c:161
↓ 2 callersFunctionbam_fillmd
samtools-1.3/bam_md.c:349
↓ 2 callersFunctionbam_fillmd1_core
samtools-1.3/bam_md.c:46
↓ 2 callersFunctionbam_lplbuf_push
samtools-1.3/bam_lpileup.c:220
↓ 2 callersFunctionbam_plbuf_destroy
samtools-1.3/bam_plbuf.c:51
↓ 2 callersFunctionbam_plbuf_init
samtools-1.3/bam_plbuf.c:41
↓ 2 callersFunctionbam_prb_to_mapq
sam_utils.h:72
↓ 2 callersFunctionbam_reg2bin
! @abstract Calculate the minimum bin that contains a region [beg,end). @param beg start of the region, 0-based @param end end of the reg
samtools-1.3/bam.h:557
↓ 2 callersFunctionbam_smpl_rg2smid
samtools-1.3/sample.c:122
↓ 2 callersFunctionbam_sort_core_ext
! @abstract Sort an unsorted BAM file based on the chromosome order and the leftmost position of an alignment @param is_by_qname whether to so
samtools-1.3/bam_sort.c:1638
↓ 2 callersFunctionbase_tv_destroy
samtools-1.3/bam_tview.c:102
↓ 2 callersFunctionbase_tv_init
samtools-1.3/bam_tview.c:57
↓ 2 callersFunctionbcf1_sync
samtools-1.3/htslib-1.3/vcf.c:1031
↓ 2 callersFunctionbcf1_sync_alleles
samtools-1.3/htslib-1.3/vcf.c:993
↓ 2 callersFunctionbcf1_sync_filter
samtools-1.3/htslib-1.3/vcf.c:1001
↓ 2 callersFunctionbcf1_sync_id
samtools-1.3/htslib-1.3/vcf.c:987
↓ 2 callersFunctionbcf1_sync_info
samtools-1.3/htslib-1.3/vcf.c:1008
↓ 2 callersFunctionbcf_call2bcf
samtools-1.3/bam2bcf.c:697
↓ 2 callersFunctionbcf_call_combine
* bcf_call_combine() - sets the PL array and VDB, RPB annotations, finds the top two alleles * @n: number of samples * @calls: each s
samtools-1.3/bam2bcf.c:526
↓ 2 callersFunctionbcf_call_destroy
samtools-1.3/bam2bcf.c:68
↓ 2 callersFunctionbcf_call_init
samtools-1.3/bam2bcf.c:43
↓ 2 callersFunctionbcf_callaux_clean
samtools-1.3/bam2bcf.c:116
↓ 2 callersFunctionbcf_dec_int1
samtools-1.3/htslib-1.3/htslib/vcf.h:875
↓ 2 callersFunctionbcf_enc_vfloat
samtools-1.3/htslib-1.3/vcf.c:1455
↓ 2 callersFunctionbcf_fmt_sized_array
samtools-1.3/htslib-1.3/vcf.c:1506
↓ 2 callersFunctionbcf_hdr_parse_sample_line
samtools-1.3/htslib-1.3/vcf.c:94
↓ 2 callersFunctionbcf_hdr_set_idx
samtools-1.3/htslib-1.3/vcf.c:344
↓ 2 callersFunctionbcf_hrec_add_key
samtools-1.3/htslib-1.3/vcf.c:204
↓ 2 callersFunctionbcf_hrec_set_val
samtools-1.3/htslib-1.3/vcf.c:216
↓ 2 callersFunctionbcf_index_build
samtools-1.3/htslib-1.3/vcf.c:2263
↓ 2 callersFunctionbcf_read
samtools-1.3/htslib-1.3/vcf.c:970
↓ 2 callersFunctionbcf_read1_core
samtools-1.3/htslib-1.3/vcf.c:899
↓ 2 callersFunctionbcf_remove_allele_set
samtools-1.3/htslib-1.3/vcfutils.c:226
↓ 2 callersFunctionbcf_set_variant_types
samtools-1.3/htslib-1.3/vcf.c:2753
↓ 2 callersFunctionbcf_sr_destroy1
samtools-1.3/htslib-1.3/synced_bcf_reader.c:268
↓ 2 callersFunctionbcf_sr_regions_init
samtools-1.3/htslib-1.3/synced_bcf_reader.c:997
↓ 2 callersFunctionbcf_sr_regions_overlap
samtools-1.3/htslib-1.3/synced_bcf_reader.c:1250
↓ 2 callersFunctionbcf_subset_format
samtools-1.3/htslib-1.3/vcf.c:929
↓ 2 callersFunctionbcf_sweep_bwd
samtools-1.3/htslib-1.3/vcf_sweep.c:174
↓ 2 callersFunctionbcf_sweep_fwd
samtools-1.3/htslib-1.3/vcf_sweep.c:145
↓ 2 callersFunctionbcf_update_id
samtools-1.3/htslib-1.3/vcf.c:3126
↓ 2 callersFunctionbcf_update_info
samtools-1.3/htslib-1.3/vcf.c:2783
↓ 2 callersFunctionbcf_write
samtools-1.3/htslib-1.3/vcf.c:1201
↓ 2 callersFunctionbessel_i0
boost/math/special_functions/detail/bessel_i0.hpp:52
↓ 2 callersFunctionbessel_i1
boost/math/special_functions/detail/bessel_i1.hpp:52
↓ 2 callersFunctionbessel_i_small_z_series
boost/math/special_functions/detail/bessel_ik.hpp:53
↓ 2 callersFunctionbessel_ik
boost/math/special_functions/detail/bessel_ik.hpp:297
↓ 2 callersFunctionbessel_jn
boost/math/special_functions/detail/bessel_jn.hpp:27
↓ 2 callersFunctionbessel_kn
boost/math/special_functions/detail/bessel_kn.hpp:23
↓ 2 callersFunctionbessel_yn_small_z
boost/math/special_functions/detail/bessel_jy_series.hpp:213
↓ 2 callersMethodbeta
Returns the "beta" parameter of the distribution. */
boost/random/gamma_distribution.hpp:134
↓ 2 callersFunctionbgzf_compress
samtools-1.3/htslib-1.3/bgzf.c:232
↓ 2 callersFunctionbgzf_getline
samtools-1.3/htslib-1.3/bgzf.c:902
↓ 2 callersFunctionbgzf_index_add_block
samtools-1.3/htslib-1.3/bgzf.c:954
↓ 2 callersFunctionbgzf_index_destroy
samtools-1.3/htslib-1.3/bgzf.c:936
↓ 2 callersFunctionbgzf_seek
samtools-1.3/htslib-1.3/bgzf.c:848
↓ 2 callersFunctionbisect
boost/math/tools/roots.hpp:97
↓ 2 callersFunctionblksize
samtools-1.3/htslib-1.3/hfile.c:416
↓ 2 callersFunctionboost_range_silence_warning
boost/range/detail/implementation_help.hpp:29
↓ 2 callersFunctionbracket_and_solve_root
boost/math/tools/toms748_solve.hpp:480
↓ 2 callersFunctionbuild_wiggles
wiggle.cpp:39
↓ 2 callersMethodc
Returns the @c c parameter of the distribution */
boost/random/triangle_distribution.hpp:132
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