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Functions5,402 in github.com/deweylab/RSEM

⨍ Functions 5,402◇ Types & classes 14,945
↓ 1 callersFunctionasinh
boost/math/special_functions/asinh.hpp:93
↓ 1 callersFunctionasinh_imp
boost/math/special_functions/asinh.hpp:46
↓ 1 callersFunctionassemble_command
utils.h:159
↓ 1 callersFunctionassign_expr_to_initialized
boost/optional/optional.hpp:370
↓ 1 callersMethodassign_from_iter
boost/fusion/container/list/cons.hpp:54
↓ 1 callersMethodassign_from_iter
boost/fusion/container/list/cons.hpp:132
↓ 1 callersFunctionasymptotic_bessel_i_large_x
boost/math/special_functions/detail/bessel_jy_asym.hpp:174
↓ 1 callersFunctionasymptotic_bessel_j_large_x_2
boost/math/special_functions/detail/bessel_jy_asym.hpp:94
↓ 1 callersFunctionatanh_imp
boost/math/special_functions/atanh.hpp:48
↓ 1 callersFunctionatomic_compare_exchange
boost/smart_ptr/shared_ptr.hpp:990
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_snc_ps3.hpp:63
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_vacpp_ppc.hpp:55
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_gcc_sparc.hpp:68
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_acc_ia64.hpp:47
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_gcc_ppc.hpp:79
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_gcc_mips.hpp:77
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp:69
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_spin.hpp:45
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_cw_ppc.hpp:71
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_gcc_ia64.hpp:57
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_sync.hpp:51
↓ 1 callersFunctionatomic_conditional_increment
boost/smart_ptr/detail/sp_counted_base_aix.hpp:53
↓ 1 callersFunctionatomic_exchange
boost/smart_ptr/shared_ptr.hpp:974
↓ 1 callersFunctionatomic_load
boost/smart_ptr/shared_ptr.hpp:952
↓ 1 callersFunctionatomic_store
boost/smart_ptr/shared_ptr.hpp:963
↓ 1 callersFunctionaux_fields1
samtools-1.3/htslib-1.3/test/sam.c:70
↓ 1 callersFunctionbad_lexical_cast
boost/lexical_cast.hpp:99
↓ 1 callersFunctionbam2fq_mainloop
samtools-1.3/sam_view.c:982
↓ 1 callersFunctionbam2fq_mainloop_singletontrack
samtools-1.3/sam_view.c:909
↓ 1 callersFunctionbam_aux_drop_other
samtools-1.3/bam_aux.c:47
↓ 1 callersFunctionbam_aux_getCQi
! @abstract Get the color quality of the color encoding the previous and current base @param b pointer to an alignment @param i The i
samtools-1.3/bam_color.c:65
↓ 1 callersFunctionbam_aux_ntnt2cs
samtools-1.3/bam_color.c:107
↓ 1 callersFunctionbam_cat
samtools-1.3/bam_cat.c:415
↓ 1 callersFunctionbam_construct_seq
--------------------------------------------------------------------------- * Samtools compatibility portion */
samtools-1.3/htslib-1.3/cram/cram_samtools.c:43
↓ 1 callersFunctionbam_flagstat
samtools-1.3/bam_stat.c:99
↓ 1 callersFunctionbam_flagstat_core
samtools-1.3/bam_stat.c:69
↓ 1 callersFunctionbam_format1
samtools-1.3/bam.c:33
↓ 1 callersFunctionbam_header_to_cram
samtools-1.3/htslib-1.3/cram/cram_samtools.c:147
↓ 1 callersFunctionbam_idxstats
samtools-1.3/bam_index.c:85
↓ 1 callersFunctionbam_index
samtools-1.3/bam_index.c:50
↓ 1 callersFunctionbam_index
samtools-1.3/htslib-1.3/sam.c:467
↓ 1 callersFunctionbam_is_proper
sam_utils.h:48
↓ 1 callersFunctionbam_iter_destroy
samtools-1.3/bam.h:480
↓ 1 callersFunctionbam_iter_query
samtools-1.3/bam.h:478
↓ 1 callersFunctionbam_iter_read
samtools-1.3/bam.h:479
↓ 1 callersFunctionbam_lplbuf_destroy
samtools-1.3/bam_lpileup.c:204
↓ 1 callersFunctionbam_lplbuf_init
samtools-1.3/bam_lpileup.c:192
↓ 1 callersFunctionbam_lplbuf_reset
samtools-1.3/bam_lpileup.c:86
↓ 1 callersFunctionbam_mating
samtools-1.3/bam_mate.c:316
↓ 1 callersFunctionbam_mating_core
currently, this function ONLY works if each read has one hit
samtools-1.3/bam_mate.c:180
↓ 1 callersFunctionbam_merge
samtools-1.3/bam_sort.c:1389
↓ 1 callersFunctionbam_mpileup
samtools-1.3/bam_plcmd.c:846
↓ 1 callersFunctionbam_mplp_init_overlaps
samtools-1.3/htslib-1.3/sam.c:2012
↓ 1 callersFunctionbam_pad2unpad
samtools-1.3/padding.c:185
↓ 1 callersFunctionbam_plbuf_reset
samtools-1.3/bam_plbuf.c:36
↓ 1 callersFunctionbam_plp_init_overlaps
samtools-1.3/htslib-1.3/sam.c:1631
↓ 1 callersFunctionbam_plp_reset
samtools-1.3/htslib-1.3/sam.c:1962
↓ 1 callersFunctionbam_reheader
* Reads a file and outputs a new BAM file to fd with 'h' replaced as * the header. No checks are made to the validity. */
samtools-1.3/bam_reheader.c:43
↓ 1 callersFunctionbam_remove_B
samtools-1.3/bam.c:143
↓ 1 callersFunctionbam_rmdup
samtools-1.3/bam_rmdup.c:216
↓ 1 callersFunctionbam_rmdup_core
samtools-1.3/bam_rmdup.c:117
↓ 1 callersFunctionbam_rmdupse_core
samtools-1.3/bam_rmdupse.c:124
↓ 1 callersFunctionbam_smpl_add
samtools-1.3/sample.c:77
↓ 1 callersFunctionbam_smpl_destroy
samtools-1.3/sample.c:41
↓ 1 callersFunctionbam_smpl_init
samtools-1.3/sample.c:32
↓ 1 callersFunctionbam_sort
samtools-1.3/bam_sort.c:1760
↓ 1 callersFunctionbam_swap_endian_2
samtools-1.3/bam_endian.h:35
↓ 1 callersFunctionbam_swap_endian_4
samtools-1.3/bam_endian.h:44
↓ 1 callersFunctionbam_swap_endian_8
samtools-1.3/bam_endian.h:54
↓ 1 callersFunctionbam_template_cigar
* This function calculates ct tag for two bams, it assumes they are from the same template and * writes the tag to the first read in position terms.
samtools-1.3/bam_mate.c:40
↓ 1 callersFunctionbam_tview_main
samtools-1.3/bam_tview.c:353
↓ 1 callersFunctionbam_write1
samtools-1.3/htslib-1.3/sam.c:435
↓ 1 callersFunctionbamshuf
samtools-1.3/bamshuf.c:77
↓ 1 callersFunctionbase64_kput
samtools-1.3/htslib-1.3/hfile_libcurl.c:648
↓ 1 callersFunctionbasic_unescape
Converts \t and \n into real tabs and newlines
samtools-1.3/bam_addrprg.c:86
↓ 1 callersFunctionbcf_add_filter
samtools-1.3/htslib-1.3/vcf.c:3012
↓ 1 callersFunctionbcf_call_add_rg
samtools-1.3/bam2bcf_indel.c:41
↓ 1 callersFunctionbcf_call_del_rghash
samtools-1.3/bam2bcf_indel.c:77
↓ 1 callersFunctionbcf_call_gap_prep
notes: - n .. number of samples - the routine sets bam_pileup1_t.aux of each read as follows: - 6: unused - 6:
samtools-1.3/bam2bcf_indel.c:147
↓ 1 callersFunctionbcf_clear
samtools-1.3/htslib-1.3/vcf.c:851
↓ 1 callersFunctionbcf_copy
samtools-1.3/htslib-1.3/vcf.c:1173
↓ 1 callersFunctionbcf_dup
samtools-1.3/htslib-1.3/vcf.c:1195
↓ 1 callersFunctionbcf_format_gt
samtools-1.3/htslib-1.3/htslib/vcf.h:803
↓ 1 callersFunctionbcf_get_fmt
samtools-1.3/htslib-1.3/vcf.c:3167
↓ 1 callersFunctionbcf_get_fmt_id
samtools-1.3/htslib-1.3/vcf.c:3181
↓ 1 callersFunctionbcf_get_format_values
samtools-1.3/htslib-1.3/vcf.c:3321
↓ 1 callersFunctionbcf_get_info
samtools-1.3/htslib-1.3/vcf.c:3174
↓ 1 callersFunctionbcf_get_info_id
samtools-1.3/htslib-1.3/vcf.c:3192
↓ 1 callersFunctionbcf_get_info_values
samtools-1.3/htslib-1.3/vcf.c:3204
↓ 1 callersFunctionbcf_hdr_check_sanity
samtools-1.3/htslib-1.3/vcf.c:564
↓ 1 callersFunctionbcf_hdr_dup
samtools-1.3/htslib-1.3/vcf.c:2523
↓ 1 callersFunctionbcf_hdr_get_version
samtools-1.3/htslib-1.3/vcf.c:720
↓ 1 callersFunctionbcf_hdr_register_hrec
returns: 1 when hdr needs to be synced, 0 otherwise
samtools-1.3/htslib-1.3/vcf.c:366
↓ 1 callersFunctionbcf_hdr_seqnames
samtools-1.3/htslib-1.3/vcf.c:1378
↓ 1 callersFunctionbcf_hdr_set_version
samtools-1.3/htslib-1.3/vcf.c:731
↓ 1 callersFunctionbcf_index
samtools-1.3/htslib-1.3/vcf.c:2206
↓ 1 callersFunctionbcf_index_build2
samtools-1.3/htslib-1.3/vcf.c:2248
↓ 1 callersFunctionbcf_set_variant_type
samtools-1.3/htslib-1.3/vcf.c:2693
↓ 1 callersFunctionbcf_sr_regions_flush
samtools-1.3/htslib-1.3/synced_bcf_reader.c:1278
↓ 1 callersFunctionbcf_sr_regions_seek
samtools-1.3/htslib-1.3/synced_bcf_reader.c:1089
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