repository

Index

Symbols

..bisect module ..collections module ..functools module ..getopt module ..gzip module ..heapq module ..itertools module ..math module ..openmp module ..operator module

..pickle module ..python module ..random module ..sortedlist module ..statistics module ..string module ..sys module ..threading module ..time module

_

__len__ (bio.bed.BEDRecord attribute)

_bcf_hdr (bio.vcf.BCFReader attribute) _n_holes (bio.fmindex.bntseq attribute)

A

A (bio.bam.SAMAux attribute) abs() (in module ..operator) (in module internal.builtin) accumulate (class in ..itertools) acos() (in module ..math) (in module internal.c_stubs) acosh() (in module ..math) (in module internal.c_stubs) acquire() (..threading.Lock method) (..threading.RLock method) active_count() (in module ..threading) add() (..sortedlist.SortedList method) (bio.intervals.IntervalTree method) (bio.seq.BaseCounts method) (in module ..operator) (internal.__init_test__.Set method) (internal.types.collections.set.Set method) add_roots() (in module internal.gc) adjust_indices() (internal.types.slice.Slice method) adjust_indices_helper() (internal.types.slice.Slice method) algorithms module algorithms.heapsort module algorithms.insertionsort module algorithms.pdqsort module algorithms.qsort module algorithms.strings module algorithms.timsort module align() (bio.align.pseq method) (bio.align.seq method) (bio.bwa.BWA method) Alignment (class in bio.align) all() (in module internal.builtin) alleles (bio.vcf.VCFRecordSample attribute) alloc() (in module internal.gc) alloc_atomic() (in module internal.gc) alt (bio.bwa.mem_aln_t attribute) alt_score (bio.bwa.mem_aln_t attribute) (bio.bwa.mem_alnreg_t attribute)

alts (bio.vcf.VCFRecord attribute) and_() (in module ..operator) any() (in module internal.builtin) append() (..collections.deque method) (internal.types.collections.list.List method) appendleft() (..collections.deque method) argv (in module ..sys) arr (bio.vcf.BCFAux attribute) Array (class in internal.types.ptr) array (in module internal.types.array) as_byte() (internal.types.ptr.Ptr method) as_int() (bio.kmer.Kmer method) ascii_letters (in module ..string) ascii_lowercase (in module ..string) ascii_uppercase (in module ..string) asin() (in module ..math) (in module internal.c_stubs) asinh() (in module ..math) (in module internal.c_stubs) AssertionError associative() (in module internal.attributes) atan() (in module ..math) (in module internal.c_stubs) atan2() (in module ..math) (in module internal.c_stubs) atanh() (in module ..math) (in module internal.c_stubs) atoi() (in module internal.c_stubs) atomic() (in module internal.gc) AttributeError attrs (bio.vcf.BCFHeaderRecord attribute) aux() (bio.bam.SAMRecord method) AUX_TYPE_ARRAY (in module bio.bam) AUX_TYPE_CHAR (in module bio.bam) AUX_TYPE_DOUBLE (in module bio.bam) AUX_TYPE_FLOAT (in module bio.bam) AUX_TYPE_INT (in module bio.bam) AUX_TYPE_INT16 (in module bio.bam) AUX_TYPE_INT32 (in module bio.bam) AUX_TYPE_INT8 (in module bio.bam) AUX_TYPE_STRING (in module bio.bam) AUX_TYPE_UINT16 (in module bio.bam) AUX_TYPE_UINT32 (in module bio.bam) AUX_TYPE_UINT8 (in module bio.bam)

B

B2f() (bio.bam.SAMAux method) B2i() (bio.bam.SAMAux method) B_len (bio.bam.SAMAux attribute) BAM() (in module bio.bam) bam_aux2A() (in module bio.c_htslib) bam_aux2f() (in module bio.c_htslib) bam_aux2i() (in module bio.c_htslib) bam_aux2Z() (in module bio.c_htslib) bam_aux_get() (in module bio.c_htslib) bam_auxB2f() (in module bio.c_htslib) bam_auxB2i() (in module bio.c_htslib) bam_auxB_len() (in module bio.c_htslib) bam_cigar2qlen() (in module bio.c_htslib) bam_cigar2rlen() (in module bio.c_htslib) bam_destroy1() (in module bio.c_htslib) bam_endpos() (in module bio.c_htslib) BAM_FDUP (in module bio.bam) BAM_FMREVERSE (in module bio.bam) BAM_FMUNMAP (in module bio.bam) BAM_FPAIRED (in module bio.bam) BAM_FPROPER_PAIR (in module bio.bam) BAM_FQCFAIL (in module bio.bam) BAM_FREAD1 (in module bio.bam) BAM_FREAD2 (in module bio.bam) BAM_FREVERSE (in module bio.bam) BAM_FSECONDARY (in module bio.bam) BAM_FSUPPLEMENTARY (in module bio.bam) BAM_FUNMAP (in module bio.bam) bam_init1() (in module bio.c_htslib) bam_read1() (in module bio.c_htslib) BAMReader (class in bio.bam) base() (in module bio.builtin) BaseCounts (class in bio.seq) bases (bio.seq.seq attribute) BCF() (in module bio.vcf) bcf_array_to_object() (in module bio.vcf) BCF_AUX_NONE (in module bio.vcf) BCF_BT_CHAR (in module bio.vcf) BCF_BT_FLOAT (in module bio.vcf) BCF_BT_INT16 (in module bio.vcf) BCF_BT_INT32 (in module bio.vcf) BCF_BT_INT8 (in module bio.vcf) BCF_BT_NULL (in module bio.vcf) bcf_clear() (in module bio.c_htslib) bcf_destroy() (in module bio.c_htslib) BCF_DT_CTG (in module bio.vcf) BCF_DT_ID (in module bio.vcf) BCF_DT_SAMPLE (in module bio.vcf) bcf_dup() (in module bio.c_htslib) bcf_empty() (in module bio.c_htslib) bcf_float_is_missing() (in module bio.vcf) bcf_float_is_vector_end() (in module bio.vcf) bcf_float_missing (in module bio.vcf) bcf_float_vector_end (in module bio.vcf) bcf_get_fmt() (in module bio.c_htslib) bcf_get_fmt_id() (in module bio.c_htslib) bcf_get_format_values() (in module bio.c_htslib) bcf_get_info() (in module bio.c_htslib) bcf_get_info_id() (in module bio.c_htslib) bcf_get_info_values() (in module bio.c_htslib) bcf_get_value_count() (in module bio.vcf) bcf_get_variant_type() (in module bio.c_htslib) bcf_get_variant_types() (in module bio.c_htslib) bcf_gt_allele() (in module bio.vcf) bcf_has_filter() (in module bio.c_htslib), [1] bcf_hdr_destroy() (in module bio.c_htslib) bcf_hdr_id2int() (in module bio.c_htslib) bcf_hdr_read() (in module bio.c_htslib) BCF_HL_CTG (in module bio.vcf) BCF_HL_FLT (in module bio.vcf) BCF_HL_FMT (in module bio.vcf) BCF_HL_GEN (in module bio.vcf) BCF_HL_INFO (in module bio.vcf) BCF_HL_STR (in module bio.vcf) bcf_hrec_format() (in module bio.c_htslib) BCF_HT_FLAG (in module bio.vcf) BCF_HT_INT (in module bio.vcf) BCF_HT_REAL (in module bio.vcf) BCF_HT_STR (in module bio.vcf) bcf_info_get_value() (in module bio.vcf) bcf_init() (in module bio.c_htslib) bcf_int16_missing (in module bio.vcf) bcf_int16_vector_end (in module bio.vcf) bcf_int32_missing (in module bio.vcf) bcf_int32_vector_end (in module bio.vcf) bcf_int8_missing (in module bio.vcf) bcf_int8_vector_end (in module bio.vcf) bcf_is_snp() (in module bio.c_htslib) bcf_read() (in module bio.c_htslib) bcf_str_missing (in module bio.vcf) bcf_str_vector_end (in module bio.vcf) bcf_type (bio.vcf.BCFMetadata attribute) BCF_UN_ALL (in module bio.vcf) BCF_UN_FLT (in module bio.vcf) BCF_UN_FMT (in module bio.vcf) BCF_UN_IND (in module bio.vcf) BCF_UN_INFO (in module bio.vcf)

BCF_UN_SHR (in module bio.vcf) BCF_UN_STR (in module bio.vcf) bcf_unpack() (in module bio.c_htslib) BCF_VL_A (in module bio.vcf) BCF_VL_FIXED (in module bio.vcf) BCF_VL_G (in module bio.vcf) BCF_VL_R (in module bio.vcf) BCF_VL_VAR (in module bio.vcf) BCFAux (class in bio.vcf) BCFHeader (class in bio.vcf) BCFHeaderContigs (class in bio.vcf) BCFHeaderMetaData (class in bio.vcf) BCFHeaderRecord (class in bio.vcf) BCFHeaderSamples (class in bio.vcf) BCFMetadata (class in bio.vcf) BCFReader (class in bio.vcf) BED() (in module bio.bed) BEDReader (class in bio.bed) BEDRecord (class in bio.bed) betavariate() (..random.Random method) (in module ..random) biinterval() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) biloci() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) bio module bio.align module bio.bam module bio.bed module bio.block module bio.builtin module bio.bwa module bio.bwt module bio.c_htslib module bio.fai module bio.fasta module bio.fastq module bio.fmindex module bio.intervals module bio.iter module bio.kmer module bio.locus module bio.prefetch module bio.pseq module bio.seq module bio.types module bio.vcf module biresults() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) bisect() (in module ..bisect) bisect_left() (in module ..bisect) bisect_right() (in module ..bisect) bit_length() (..random.Random method) biupdate() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) Block (class in bio.block) block_count (bio.bed.BEDRecord attribute) BLOCK_SIZE (in module algorithms.timsort) block_sizes (bio.bed.BEDRecord attribute) block_starts (bio.bed.BEDRecord attribute) blocks() (in module bio.block) bntamb (class in bio.fmindex) bntamb1_t (class in bio.bwa) bntann (class in bio.fmindex) bntann1_t (class in bio.bwa) bntseq (class in bio.fmindex) bntseq_t (class in bio.bwa) Box (class in internal.box) BWA (class in bio.bwa) bwa_fill_scmat() (in module bio.bwa) bwa_idx_load() (in module bio.bwa) BWA_LIB (in module bio.bwa) bwaidx_t (class in bio.bwa) bwt() (bio.bwt.pseq method) (bio.bwt.seq method)

C

C() (in module internal.attributes) c_dlclose() (in module internal.dlopen) c_dlerror() (in module internal.dlopen) c_dlopen() (in module internal.dlopen) c_dlsym() (in module internal.dlopen) c_str() (internal.types.str.str method) CACHELINE_SIZE (in module algorithms.timsort) canonical() (in module bio.builtin) canonical_with_pos() (in module bio.builtin) capitalize() (internal.str.str method) casefold() (internal.str.str method) cat() (internal.types.str.str method) cdf() (..statistics.NormalDist method) ceil() (in module ..math) (in module internal.c_stubs) center() (internal.str.str method) CError chain (class in ..itertools) char_p (in module bio.vcf) char_pp (in module bio.vcf) check_header_id() (in module bio.vcf) check_N() (in module internal.types.intn) choice() (..random.Random method) (in module ..random) choices() (..random.Random method) (in module ..random) chr() (in module internal.builtin) chrom (bio.bed.BEDRecord attribute) (bio.vcf.VCFRecord attribute) chrom_end (bio.bed.BEDRecord attribute) chrom_start (bio.bed.BEDRecord attribute) cigar (bio.align.Alignment attribute) (bio.bam.SAMRecord attribute) (bio.bwa.mem_aln_t attribute) CIGAR (class in bio.align) clear() (..collections.deque method) (..sortedlist.SortedList method) (internal.types.collections.dict.Dict method) (internal.types.collections.list.List method) (internal.types.collections.set.Set method) clear_roots() (in module internal.gc) close() (bio.bam.BAMReader method) (bio.bam.SAMReader method) (bio.bed.BEDReader method) (bio.fai.FAIReader method) (bio.fasta.FASTAReader method) (bio.fasta.pFASTAReader method) (bio.fastq.FASTQReader method) (bio.iter.SeqReader method) (bio.vcf.BCFReader method) (internal.file.File method) (internal.file.gzFile method)

cnt_ambi() (bio.fmindex.bntseq method) cobj (in module internal.types.ptr) combinations() (in module ..itertools) combinations_with_replacement() (in module ..itertools) comment (bio.fasta.FASTARecord attribute) (bio.fastq.FASTQRecord attribute) commutative() (in module internal.attributes) comp() (bio.types.byte method) compress() (in module ..itertools) computeLPArray() (in module algorithms.strings) concat() (in module ..operator) contains() (in module ..operator) contig (bio.vcf.VCFRecord attribute) Contig (class in bio.locus) contig() (bio.bam.BAMReader method) (bio.bam.SAMReader method) (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) contigs (bio.vcf.BCFHeader attribute) contigs() (bio.bam.BAMReader method) (bio.bam.SAMReader method) (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) copy() (..collections.deque method) (in module internal.builtin) (internal.types.collections.dict.Dict method) (internal.types.collections.set.Set method) copysign() (in module ..math) (in module internal.c_stubs) (internal.types.float.float method) cos() (in module ..math) (in module internal.c_stubs) (internal.types.float.float method) cosh() (in module ..math) (in module internal.c_stubs) count() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) (in module ..itertools) (internal.str.str method) (internal.types.collections.list.List method) (internal.types.range.range method) Counter (class in ..collections) countOf() (in module ..operator) CRAM() (in module bio.bam) CRAMReader (in module bio.bam) critical() (in module ..openmp) csub (bio.bwa.mem_alnreg_t attribute) cycle() (in module ..itertools)

D

decref() (internal.python.pyobj method) DEFAULT_LOAD_FACTOR (in module ..sortedlist) degrees() (in module ..math) delitem() (in module ..operator) depos() (bio.fmindex.bntseq method) deque (class in ..collections) description (bio.vcf.BCFMetadata attribute) destroy() (internal.types.generator.Generator method) Dict (class in internal.__init_test__) (class in internal.types.collections.dict) dict (in module internal.types.collections.dict) difference() (internal.types.collections.set.Set method) difference_update() (internal.types.collections.set.Set method)

digits (in module ..string) discard() (internal.types.collections.set.Set method) distributive() (in module internal.attributes) dlclose() (in module internal.dlopen) dlerror() (in module internal.dlopen) dlext() (in module internal.dlopen) dlopen() (in module internal.dlopen) dlsym() (in module internal.dlopen) do_longs() (in module ..getopt) do_shorts() (in module ..getopt) done() (internal.types.generator.Generator method) dropwhile() (in module ..itertools) dump() (in module ..pickle) duplicate (bio.bam.SAMRecord attribute)

E

e (in module ..math) echo() (in module internal.builtin) elapsed() (..time.TimeInterval method) elements() (..collections.Counter method) end (bio.intervals.Interval attribute) endpos (bio.bam.SAMRecord attribute) endswith() (internal.str.str method) ensure_initialized() (in module internal.python) enumerate() (in module internal.builtin) eq (in module ..operator) erf() (in module ..math) (in module internal.c_stubs) erfc() (in module ..math) (in module internal.c_stubs) exc_check() (internal.python.pyobj method) exc_wrap() (internal.python.pyobj method)

ExcHeader (class in internal.types.error) exclude_static_roots() (in module internal.gc) exit() (in module ..sys) (in module internal.c_stubs) (in module internal.internal) exp() (in module ..math) (in module internal.c_stubs) (internal.types.float.float method) exp2() (internal.types.float.float method) expandtabs() (internal.str.str method) expm1() (in module ..math) (in module internal.c_stubs) export() (in module internal.attributes) expovariate() (..random.Random method) (in module ..random) extend() (internal.types.collections.list.List method)

F

f (bio.bam.SAMAux attribute) fabs() (in module ..math) (in module internal.c_stubs) factorial() (in module ..math) FAI() (in module bio.fai) FAI_COL_NAMES (in module bio.fai) FAIReader (class in bio.fai) FAIRecord (class in bio.fai) FASTA() (in module bio.fasta) FASTAReader (class in bio.fasta) FASTARecord (class in bio.fasta) FASTQ() (in module bio.fastq) FASTQReader (class in bio.fastq) FASTQRecord (class in bio.fastq) fclose() (in module internal.c_stubs) ferror() (in module internal.c_stubs) fflush() (in module internal.c_stubs) fgetc() (in module internal.c_stubs) fgets() (in module internal.c_stubs) file (bio.bed.BEDReader attribute) (bio.fai.FAIReader attribute) (bio.fasta.FASTAReader attribute) (bio.fasta.pFASTAReader attribute) (bio.fastq.FASTQReader attribute) (bio.iter.SeqReader attribute) File (class in internal.file) filter() (in module internal.builtin) filter_overlaps() (in module algorithms.strings) filterfalse() (in module ..itertools) filters (bio.vcf.BCFHeader attribute)

find() (internal.str.str method) flag (bio.bam.SAMRecord attribute) floor() (in module ..math) (in module internal.c_stubs) floordiv() (in module ..operator) flush() (in module ..openmp) (internal.file.File method) fma() (internal.types.float.float method) FMDIndex (class in bio.fmindex) FMDInterval (class in bio.fmindex) FMIndex (class in bio.fmindex) FMInterval (class in bio.fmindex) fmod() (in module ..math) (in module internal.c_stubs) fopen() (in module internal.c_stubs) for_par() (in module ..openmp) formats (bio.vcf.BCFHeader attribute) forward() (bio.fmindex.FMDInterval method) fread() (in module internal.c_stubs) free() (in module internal.c_stubs) (in module internal.gc) frexp() (in module ..math) (in module internal.c_stubs) from_bytes_big() (..random.Random method) from_iterable() (..itertools.chain method) from_ptr() (internal.types.str.str method) from_samples() (..statistics.NormalDist method) fromkeys() (internal.types.collections.dict.Dict method) fseek() (in module internal.c_stubs) ftell() (in module internal.c_stubs) fwrite() (in module internal.c_stubs)

G

gamma() (in module ..math) gammavariate() (..random.Random method) (in module ..random) gauss() (..random.Random method) (in module ..random) gcd() (in module ..math) ge (in module ..operator) generator (in module internal.types.generator) genrand_int32() (..random.RandomGenerator method) genrand_res53() (..random.RandomGenerator method) geometric_mean() (in module ..statistics) get() (bio.vcf.BCFHeaderRecord method) (in module internal.python) (internal.python.pyobj method) (internal.types.collections.dict.Dict method) get_active_level() (in module ..openmp) get_ancestor_thread_num() (in module ..openmp) get_cancellation() (in module ..openmp) get_default_device() (in module ..openmp) get_dynamic() (in module ..openmp) get_flag() (bio.vcf.VCFRecordInfo method) get_float() (bio.vcf.VCFRecordInfo method) get_floats() (bio.vcf.VCFRecordInfo method) get_ident() (in module ..threading) get_int() (bio.vcf.VCFRecordInfo method) get_ints() (bio.vcf.VCFRecordInfo method) get_level() (in module ..openmp) get_max_active_levels() (in module ..openmp) get_max_threads() (in module ..openmp) get_native_id() (in module ..threading) get_num_devices() (in module ..openmp) get_num_procs() (in module ..openmp) get_num_teams() (in module ..openmp) get_num_threads() (in module ..openmp)

get_pac() (bio.fmindex.bntseq method) get_proc_bind() (in module ..openmp) get_schedule() (in module ..openmp) get_seq() (bio.fmindex.bntseq method) get_str() (bio.vcf.VCFRecordInfo method) get_team_num() (in module ..openmp) get_team_size() (in module ..openmp) get_thread_limit() (in module ..openmp) get_thread_num() (in module ..openmp) get_wtick() (in module ..openmp) get_wtime() (in module ..openmp) getitem() (in module ..operator) getline() (in module internal.c_stubs) getopt() (in module ..getopt) GetoptError getrandbits() (..random.Random method) (in module ..random) gettimeofday() (..random.RandomGenerator method) groupby() (in module ..itertools) gt (in module ..operator) gzclose() (in module internal.c_stubs) gzerror() (in module internal.c_stubs) gzfile (bio.fasta.FASTAReader attribute) (bio.fasta.pFASTAReader attribute) (bio.fastq.FASTQReader attribute) (bio.iter.SeqReader attribute) gzFile (class in internal.file) gzgetc() (in module internal.c_stubs) gzgets() (in module internal.c_stubs) gzopen() (in module internal.c_stubs) (in module internal.file) gzread() (in module internal.c_stubs) gzseek() (in module internal.c_stubs) gztell() (in module internal.c_stubs) gzwrite() (in module internal.c_stubs)

H

harmonic_mean() (in module ..statistics) hash() (in module internal.builtin) hdr_type (bio.vcf.BCFHeaderRecord attribute) header (bio.bed.BEDReader attribute) (bio.fasta.FASTARecord attribute) (bio.fastq.FASTQRecord attribute) heap_sort() (in module algorithms.heapsort) heap_sort_array() (in module algorithms.heapsort) heap_sort_inplace() (in module algorithms.heapsort) heapify() (in module ..heapq) heappop() (in module ..heapq)

heappush() (in module ..heapq) heappushpop() (in module ..heapq) heapreplace() (in module ..heapq) hexdigits (in module ..string) hts_close() (in module bio.c_htslib) hts_idx_destroy() (in module bio.c_htslib) hts_itr_destroy() (in module bio.c_htslib), [1] hts_itr_next() (in module bio.c_htslib) hts_open() (in module bio.c_htslib) hts_set_threads() (in module bio.c_htslib) hts_version() (in module bio.c_htslib) hypot() (in module ..math)

I

i (bio.bam.SAMAux attribute) i16 (in module internal.types.intn) i32 (in module internal.types.intn) i64 (in module internal.types.intn) i8 (in module internal.types.intn) iadd() (in module ..operator) iand() (in module ..operator) iconcat() (in module ..operator) id (bio.vcf.VCFRecord attribute) id() (in module internal.builtin) Ident (class in ..openmp) ifloordiv() (in module ..operator) ilshift() (in module ..operator) imatmul() (in module ..operator) imod() (in module ..operator) Import (class in internal.internal) imul() (in module ..operator) in_final() (in module ..openmp) in_parallel() (in module ..openmp) incref() (internal.python.pyobj method) increment() (internal.types.collections.dict.Dict method) index() (bio.intervals.IntervalTree method) (in module ..operator) (internal.str.str method) (internal.types.collections.list.List method) (internal.types.range.range method) IndexError indexOf() (in module ..operator) inf (in module ..math) info (bio.vcf.BCFHeader attribute) (bio.vcf.VCFRecord attribute) init() (in module internal.python) init_by_array() (..random.RandomGenerator method) init_genrand() (..random.RandomGenerator method) init_header() (bio.bed.BEDReader method) inline() (in module internal.attributes) insert() (internal.types.collections.list.List method) insert_size (bio.bam.SAMRecord attribute) insertion_sort() (in module algorithms.insertionsort) insertion_sort_array() (in module algorithms.insertionsort) insertion_sort_inplace() (in module algorithms.insertionsort) INSERTION_SORT_THRESHOLD (in module algorithms.pdqsort) insort() (in module ..bisect) insort_left() (in module ..bisect) insort_right() (in module ..bisect) INT16_MIN (in module bio.vcf) INT32_MIN (in module bio.vcf) INT8_MIN (in module bio.vcf) inter_align() (in module bio.builtin) InterAlignParams (class in bio.align) InterAlignYield (class in bio.align) internal module internal.__init_test__ module internal.attributes module internal.box module internal.builtin module internal.c_stubs module internal.dlopen module internal.file module internal.gc module internal.internal module internal.khash module internal.python module internal.sort module internal.str module internal.types module internal.types.array module internal.types.bool module internal.types.byte module

internal.types.collections module internal.types.collections.dict module internal.types.collections.list module internal.types.collections.set module internal.types.error module internal.types.float module internal.types.generator module internal.types.int module internal.types.intn module internal.types.optional module internal.types.ptr module internal.types.range module internal.types.slice module internal.types.str module intersection() (internal.types.collections.set.Set method) intersection_update() (internal.types.collections.set.Set method) interval (bio.fmindex.SMEM attribute) Interval (class in bio.intervals) interval() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) IntervalTree (class in bio.intervals) intv2rid() (bio.fmindex.bntseq method) inv() (in module ..operator) inv_cdf() (..statistics.NormalDist method) invert (in module ..operator) IOError ior() (in module ..operator) ipow() (in module ..operator) irshift() (in module ..operator) is_() (in module ..operator) is_array (bio.vcf.BCFAux attribute) is_binary() (in module internal.file) is_gt_fmt() (in module bio.vcf) is_initial_device() (in module ..openmp) is_line_header() (bio.bed.BEDReader method) is_not() (in module ..operator) isalnum() (in module internal.c_stubs) (internal.str.str method) isalpha() (in module internal.c_stubs) (internal.str.str method) isascii() (internal.str.str method) isclose() (in module ..math) isdecimal() (internal.str.str method) isdigit() (in module internal.c_stubs) (internal.str.str method) isdisjoint() (internal.types.collections.set.Set method) isfinite() (in module ..math) isidentifier() (internal.str.str method) isinf() (in module ..math) islice (class in ..itertools) islower() (in module internal.c_stubs) (internal.str.str method) isnan() (in module ..math) isnumeric() (internal.str.str method) isprintable() (internal.str.str method) isspace() (in module internal.c_stubs) (internal.str.str method) issubset() (internal.types.collections.set.Set method) issuperset() (internal.types.collections.set.Set method) istitle() (in module internal.c_stubs) (internal.str.str method) isub() (in module ..operator) isupper() (in module internal.c_stubs) (internal.str.str method) item_rgb (bio.bed.BEDRecord attribute) itemgetter() (in module ..operator) items() (internal.__init_test__.Dict method) (internal.types.collections.dict.Dict method) iter() (in module internal.builtin) iteritems() (bio.vcf.BCFHeaderRecord method) iterkeys() (bio.vcf.BCFHeaderRecord method) itervalues() (bio.vcf.BCFHeaderRecord method) itruediv() (in module ..operator) ixor() (in module ..operator)

J

Jar (in module internal.types.ptr)

join() (internal.str.str method), [1]

K

key (bio.vcf.BCFHeaderRecord attribute) KeyError keys() (internal.types.collections.dict.Dict method) Kmer (class in bio.seq) kmers() (bio.seq.seq method) (in module bio.builtin)

kmers_canonical() (bio.seq.seq method) kmers_canonical_with_pos() (bio.seq.seq method) kmers_with_pos() (bio.seq.seq method) (in module bio.builtin)

L

lcp() (bio.bwt.seq method) ldexp() (in module ..math) (in module internal.c_stubs) le (in module ..operator) left (..collections.deque attribute) (..sortedlist.SortedList attribute) len (bio.locus.Contig attribute) len() (bio.kmer.Kmer method) (in module internal.builtin) (internal.types.intn.Int method) (internal.types.intn.UInt method) length (bio.fai.FAIRecord attribute) length_hint() (in module ..operator) less() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) lgamma() (in module ..math) (in module internal.c_stubs) line_bases (bio.fai.FAIRecord attribute) line_width (bio.fai.FAIRecord attribute) List (class in internal.types.ptr) list (in module internal.types.collections.list) ljust() (internal.str.str method) load() (in module ..pickle) locate() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method)

loci() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) Lock (class in ..openmp) (class in ..threading) locus (bio.bam.SAMRecord attribute) Locus (class in bio.locus) log() (in module ..math) (in module internal.c_stubs) (internal.types.float.float method) log10() (in module ..math) (in module internal.c_stubs) (internal.types.float.float method) log1p() (in module ..math) (in module internal.c_stubs) log2() (in module ..math) (in module internal.c_stubs), [1] (internal.types.float.float method) LOG4 (in module ..random) lognormvariate() (..random.Random method) (in module ..random) long_has_args() (in module ..getopt) lower() (internal.str.str method) LRData (class in ..openmp) lshift() (in module ..operator) lstrip() (internal.str.str method) lt (in module ..operator)

M

M (in module ..random) map() (in module internal.builtin) mapq (bio.bam.SAMRecord attribute) (bio.bwa.mem_aln_t attribute) master() (in module ..openmp) mate_locus (bio.bam.SAMRecord attribute) mate_pos (bio.bam.SAMRecord attribute) mate_reversed (bio.bam.SAMRecord attribute) mate_tid (bio.bam.SAMRecord attribute) mate_unmapped (bio.bam.SAMRecord attribute) matmul() (in module ..operator) max() (in module internal.builtin) (internal.types.float.float method) maxlen (..collections.deque attribute) maxsize (in module ..sys) mean (..statistics.NormalDist attribute) mean() (in module ..statistics) median (..statistics.NormalDist attribute) median() (in module ..statistics) median_grouped() (in module ..statistics) median_high() (in module ..statistics) median_low() (in module ..statistics) mem_align1() (in module bio.bwa) mem_aln_t (class in bio.bwa) mem_alnreg_t (class in bio.bwa) mem_alnreg_v (class in bio.bwa) mem_opt_init() (in module bio.bwa) mem_reg2aln() (in module bio.bwa) memcpy() (internal.types.str.str method) memmove() (internal.types.str.str method) memset() (internal.types.str.str method) message (..getopt.GetoptError attribute) (..statistics.StatisticsError attribute) (internal.types.error.AssertionError attribute) (internal.types.error.AttributeError attribute) (internal.types.error.CError attribute) (internal.types.error.IndexError attribute) (internal.types.error.IOError attribute) (internal.types.error.KeyError attribute) (internal.types.error.NotImplementedError attribute) (internal.types.error.OSError attribute) (internal.types.error.PyError attribute) (internal.types.error.StopIteration attribute) (internal.types.error.SystemExit attribute) (internal.types.error.TypeError attribute) (internal.types.error.ValueError attribute) (internal.types.error.ZeroDivisionError attribute) METADATA_TYPES (in module bio.vcf) min() (in module internal.builtin) (internal.types.float.float method) MIN_GALLOP (in module algorithms.timsort) misc (bio.bed.BEDRecord attribute) mod() (in module ..operator) mode (..statistics.NormalDist attribute) mode() (in module ..statistics) modf() (in module ..math) (in module internal.c_stubs) module ..bisect ..collections ..functools ..getopt ..gzip ..heapq ..itertools ..math ..openmp ..operator ..pickle ..python ..random ..sortedlist ..statistics ..string ..sys ..threading ..time algorithms algorithms.heapsort algorithms.insertionsort algorithms.pdqsort algorithms.qsort algorithms.strings algorithms.timsort bio bio.align bio.bam bio.bed bio.block bio.builtin bio.bwa bio.bwt bio.c_htslib bio.fai bio.fasta bio.fastq bio.fmindex bio.intervals bio.iter bio.kmer bio.locus bio.prefetch bio.pseq bio.seq bio.types bio.vcf internal internal.__init_test__ internal.attributes internal.box internal.builtin internal.c_stubs internal.dlopen internal.file internal.gc internal.internal internal.khash internal.python internal.sort internal.str internal.types internal.types.array internal.types.bool internal.types.byte internal.types.collections internal.types.collections.dict internal.types.collections.list internal.types.collections.set internal.types.error internal.types.float internal.types.generator internal.types.int internal.types.intn internal.types.optional internal.types.ptr internal.types.range internal.types.slice internal.types.str os os.path

most_common() (..collections.Counter method) mul() (in module ..operator) multimode() (in module ..statistics)

N

N (in module ..random) N() (bio.seq.seq method) n_info (bio.vcf.VCFRecord attribute) name (bio.bam.SAMRecord attribute) (bio.fai.FAIRecord attribute) (bio.fasta.FASTARecord attribute) (bio.fasta.pFASTARecord attribute) (bio.fastq.FASTQRecord attribute) (bio.locus.Contig attribute) (bio.vcf.BCFMetadata attribute) (bio.vcf.VCFRecordSample attribute) name() (bio.bwa.BWA method) (bio.bwa.bwaidx_t method) namedtuple() (in module ..collections) nan (in module ..math) ne (in module ..operator) nearbyint() (internal.types.float.float method) neg() (in module ..operator)

next() (in module internal.__init_test__) (in module internal.builtin) (internal.types.generator.Generator method) NINTHER_THRESHOLD (in module algorithms.pdqsort) nlargest() (in module ..heapq) NM (bio.bwa.mem_aln_t attribute) noinline() (in module internal.attributes) none() (in module internal.python) nonpure() (in module internal.attributes) NormalDist (class in ..statistics) normalvariate() (..random.Random method) (in module ..random) not_() (in module ..operator) NotImplementedError nsmallest() (in module ..heapq) num_cols (bio.bed.BEDRecord attribute) num_necessary_cols (bio.fai.FAIReader attribute) NV_MAGICCONST (in module ..random)

O

object (class in internal.builtin) occ() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) OCC_INTERVAL (in module bio.fmindex) OCC_INTV_MASK (in module bio.fmindex) OCC_INTV_SHIFT (in module bio.fmindex) octdigits (in module ..string) offset (bio.fai.FAIRecord attribute) open() (in module ..gzip) (in module internal.file) optional (in module internal.types.optional)

options() (in module bio.bwa) or_() (in module ..operator) ord() (in module internal.builtin) ordered() (in module ..openmp) os module os.path module OSError overlap() (..statistics.NormalDist method) (bio.intervals.IntervalTree method)

P

paired (bio.bam.SAMRecord attribute) paretovariate() (..random.Random method) (in module ..random) partial() (in module ..functools) PARTIAL_INSERTION_SORT_LIMIT (in module algorithms.pdqsort) partition() (internal.str.str method) pdf() (..statistics.NormalDist method) pdq_sort() (in module algorithms.pdqsort) pdq_sort_array() (in module algorithms.pdqsort) pdq_sort_inplace() (in module algorithms.pdqsort) permutations() (in module ..itertools) pFASTA() (in module bio.fasta) pFASTAReader (class in bio.fasta) pFASTARecord (class in bio.fasta) pi (in module ..math) pickle() (in module ..pickle) pop() (..collections.deque method) (internal.types.collections.dict.Dict method) (internal.types.collections.list.List method) (internal.types.collections.set.Set method) popcnt() (internal.types.int.int method) (internal.types.intn.Int method) (internal.types.intn.UInt method) popitem() (internal.types.collections.dict.Dict method) popleft() (..collections.deque method) pos (bio.bam.SAMRecord attribute) (bio.bwa.mem_aln_t attribute) (bio.locus.Locus attribute) (bio.vcf.VCFRecord attribute) pos() (in module ..operator) pos2rid() (bio.fmindex.bntseq method) pow() (in module ..math) (in module ..operator) (in module internal.c_stubs) prefetch() (bio.types.Dict method) (bio.types.List method) (in module bio.builtin) print() (in module internal.builtin) printable (in module ..string) product (class in ..itertools) proper_pair (bio.bam.SAMRecord attribute) pseq (class in bio.pseq)

pstdev() (in module ..statistics) ptr (in module internal.types.ptr) ptr_off() (in module bio.vcf) punctuation (in module ..string) pure() (in module internal.attributes) pvariance() (in module ..statistics) py() (in module internal.python) Py_DecRef (in module internal.python) Py_IncRef (in module internal.python) Py_Initialize (in module internal.python) PyBool_FromLong (in module internal.python) PyBytes_AsString (in module internal.python) PyDict_New (in module internal.python) PyDict_Next (in module internal.python) PyDict_SetItem (in module internal.python) PyErr_Fetch (in module internal.python) PyError PyFloat_AsDouble (in module internal.python) PyFloat_FromDouble (in module internal.python) PyImport_ImportModule (in module internal.python) PyIter_Next (in module internal.python) PyList_GetItem (in module internal.python) PyList_New (in module internal.python) PyList_SetItem (in module internal.python) PyLong_AsLong (in module internal.python) PyLong_FromLong (in module internal.python) PyObject_Call (in module internal.python) PyObject_GetAttr (in module internal.python) PyObject_GetAttrString (in module internal.python) PyObject_GetIter (in module internal.python) PyObject_IsTrue (in module internal.python) PyObject_Length (in module internal.python) PyObject_SetAttrString (in module internal.python) PyObject_Str (in module internal.python) PyRun_SimpleString (in module internal.python) PySet_Add (in module internal.python) PySet_New (in module internal.python) PyTuple_GetItem (in module internal.python) PyTuple_New (in module internal.python) PyTuple_SetItem (in module internal.python) PyUnicode_AsEncodedString (in module internal.python) PyUnicode_DecodeFSDefaultAndSize (in module internal.python)

Q

qb (bio.bwa.mem_alnreg_t attribute) qc_fail (bio.bam.SAMRecord attribute) qe (bio.bwa.mem_alnreg_t attribute) qlen (bio.align.CIGAR attribute) qsort() (in module algorithms.qsort) qsort_array() (in module algorithms.qsort) qsort_inplace() (in module algorithms.qsort)

qual (bio.bam.SAMRecord attribute) (bio.fastq.FASTQRecord attribute) (bio.vcf.VCFRecord attribute) qual_offset (bio.fai.FAIRecord attribute) quantiles() (..statistics.NormalDist method) (in module ..statistics) query_name (bio.bam.SAMRecord attribute)

R

radians() (in module ..math) randint() (..random.Random method) (in module ..random) Random (class in ..random) random() (..random.Random method) (in module ..random) random_seed_time_pid() (..random.RandomGenerator method) RandomGenerator (class in ..random) randrange() (..random.Random method) (in module ..random) range (class in internal.types.range) rb (bio.bwa.mem_alnreg_t attribute) re (bio.bwa.mem_alnreg_t attribute) read (bio.bam.SAMRecord attribute) (bio.fastq.FASTQRecord attribute) read() (internal.file.File method) read1 (bio.bam.SAMRecord attribute) read2 (bio.bam.SAMRecord attribute) readlines() (internal.file.File method) (internal.file.gzFile method) realloc() (in module internal.gc) record (bio.vcf.BCFMetadata attribute) ref (bio.vcf.VCFRecord attribute) reg2aln() (bio.bwa.BWA method) release() (..threading.Lock method) (..threading.RLock method) remainder() (in module ..math) (in module internal.c_stubs) remove() (internal.types.collections.list.List method) (internal.types.collections.set.Set method) remove_roots() (in module internal.gc) repeat() (in module ..itertools) replace() (internal.str.str method) replace_delete_substring() (in module algorithms.strings)

replace_interleave() (in module algorithms.strings) report() (..time.TimeInterval method) repr() (in module internal.builtin) resize() (internal.types.collections.dict.Dict method) (internal.types.collections.set.Set method) results() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) rev (bio.bwa.mem_aln_t attribute) revcomp() (bio.fmindex.FMDInterval method) (in module bio.builtin) revcomp_with_pos() (in module bio.builtin) reverse() (internal.types.collections.list.List method) reversed (bio.bam.SAMRecord attribute) (bio.locus.Locus attribute) reversed() (in module internal.builtin) rfilter_overlaps() (in module algorithms.strings) rfind() (internal.str.str method) rid (bio.bwa.mem_aln_t attribute) (bio.bwa.mem_alnreg_t attribute) rindex() (internal.str.str method) rint() (internal.types.float.float method) rjust() (internal.str.str method) rlen (bio.align.CIGAR attribute) (bio.vcf.VCFRecord attribute) RLock (class in ..threading) round() (in module internal.builtin) (in module internal.c_stubs) Routine (in module ..openmp) rpartition() (internal.str.str method) rshift() (in module ..operator) rsplit() (internal.str.str method) rstring_search_slow() (in module algorithms.strings) rstrip() (internal.str.str method) RTLD_GLOBAL (in module internal.dlopen) RTLD_NOW (in module internal.dlopen)

S

SAM() (in module bio.bam) sam_hdr_destroy() (in module bio.c_htslib) sam_hdr_read() (in module bio.c_htslib) sam_index_load() (in module bio.c_htslib) sam_itr_next() (in module bio.c_htslib) sam_itr_querys() (in module bio.c_htslib) sam_read1() (in module bio.c_htslib) SAMAux (class in bio.bam) sample() (..random.Random method) (in module ..random) samples (bio.vcf.BCFHeader attribute) samples() (..statistics.NormalDist method) SAMReader (class in bio.bam) SAMRecord (class in bio.bam) score (bio.align.Alignment attribute) (bio.bed.BEDRecord attribute) (bio.bwa.mem_aln_t attribute) (bio.bwa.mem_alnreg_t attribute) secondary (bio.bam.SAMRecord attribute) (bio.bwa.mem_alnreg_t attribute) secondary_all (bio.bwa.mem_alnreg_t attribute) seed() (..random.Random method) (..random.RandomGenerator method) (in module ..random) seedcov (bio.bwa.mem_alnreg_t attribute) seek() (bio.bam.BAMReader method) (internal.file.File method) (internal.file.gzFile method) send() (internal.types.generator.Generator method) seq (bio.bam.SAMRecord attribute) (bio.fasta.FASTARecord attribute) (bio.fasta.pFASTARecord attribute) (bio.fastq.FASTQRecord attribute) (class in bio.seq) seq_align() (in module bio.align) seq_align_default() (in module bio.align) seq_align_dual() (in module bio.align) seq_align_global() (in module bio.align) seq_align_splice() (in module bio.align) seq_alloc() (in module internal.gc) seq_alloc_atomic() (in module internal.gc) seq_check_errno() (in module internal.internal) seq_env() (in module internal.c_stubs) seq_free() (in module internal.gc) seq_gc_add_roots() (in module internal.gc) seq_gc_clear_roots() (in module internal.gc) seq_gc_exclude_static_roots() (in module internal.gc) seq_gc_remove_roots() (in module internal.gc) seq_get_htsfile_fp() (in module bio.c_htslib) seq_i32_to_float() (in module internal.c_stubs) seq_is_htsfile_bgzf() (in module bio.c_htslib) seq_is_htsfile_cram() (in module bio.c_htslib) seq_is_macos() (in module internal.dlopen) seq_lock_acquire() (in module internal.c_stubs) seq_lock_new() (in module internal.c_stubs) seq_lock_release() (in module internal.c_stubs) seq_palign() (in module bio.align) seq_palign_default() (in module bio.align) seq_palign_dual() (in module bio.align) seq_palign_global() (in module bio.align) seq_pid() (in module internal.c_stubs) seq_print() (in module internal.c_stubs) (in module internal.internal) seq_print_full() (in module internal.__init_test__) (in module internal.c_stubs) seq_realloc() (in module internal.gc) seq_rlock_acquire() (in module internal.c_stubs) seq_rlock_new() (in module internal.c_stubs) seq_rlock_release() (in module internal.c_stubs) seq_stderr() (in module internal.c_stubs) seq_stdin() (in module internal.c_stubs) seq_stdout() (in module internal.c_stubs) seq_str_byte() (in module internal.types.byte) seq_str_float() (in module internal.types.float) seq_str_int() (in module internal.types.int) seq_str_ptr() (in module internal.types.ptr) seq_str_uint() (in module internal.types.int) seq_strdup() (in module internal.c_stubs) seq_time() (in module internal.c_stubs) seq_time_monotonic() (in module internal.c_stubs)

SeqPair (class in bio.align) SeqReader (class in bio.iter) seqs() (in module bio.builtin) Seqs() (in module bio.iter) sequence() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) Set (class in internal.__init_test__) (class in internal.types.collections.set) set (in module internal.types.collections.set) set_default_device() (in module ..openmp) set_dynamic() (in module ..openmp) set_max_active_levels() (in module ..openmp) set_num_threads() (in module ..openmp) set_schedule() (in module ..openmp) setdefault() (internal.types.collections.dict.Dict method) setitem() (in module ..operator) SG_MAGICCONST (in module ..random) short_has_arg() (in module ..getopt) shuffle() (..random.Random method) (in module ..random) sin() (in module ..math) (in module internal.c_stubs) (internal.types.float.float method) single() (in module ..openmp) sinh() (in module ..math) (in module internal.c_stubs) sizeof() (in module internal.gc) Slice (class in internal.types.slice) slice (in module internal.types.slice) slice() (internal.types.array.Array method) SMEM (class in bio.fmindex) smems() (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) (in module bio.fmindex) sort() (internal.sort.List method) sorted() (in module internal.sort) SortedList (class in ..sortedlist) split() (bio.pseq.pseq method) (bio.seq.seq method) (in module bio.builtin) (internal.str.str method) splitext() (in module os.path) splitlines() (internal.str.str method) sqrt() (in module ..math) (in module internal.c_stubs) (internal.types.float.float method) starmap() (in module ..itertools) start (bio.fmindex.SMEM attribute) (bio.intervals.Interval attribute) startswith() (internal.str.str method) StatisticsError status (internal.types.error.SystemExit attribute) stderr (in module ..sys) stdev (..statistics.NormalDist attribute) stdev() (in module ..statistics) stdin (in module ..sys) stdout (in module ..sys) stop (bio.fmindex.SMEM attribute) StopIteration (class in internal.types.error) strand (bio.bed.BEDRecord attribute) string_search_KMP() (in module algorithms.strings) string_search_rabin_karp() (in module algorithms.strings) string_search_slow() (in module algorithms.strings) strip() (internal.str.str method) strlen() (in module internal.types.str) sub (bio.bwa.mem_aln_t attribute) (bio.bwa.mem_alnreg_t attribute) sub() (in module ..operator) sub_n (bio.bwa.mem_alnreg_t attribute) SubMat (class in bio.align) subtract() (..collections.Counter method), [1], [2] suffix_array() (bio.bwt.pseq method) (bio.bwt.seq method) sum() (in module internal.builtin) supplementary (bio.bam.SAMRecord attribute) swapcase() (internal.str.str method) symmetric_difference() (internal.types.collections.set.Set method) symmetric_difference_update() (internal.types.collections.set.Set method) system() (in module internal.c_stubs) SystemExit (class in internal.types.error)

T

tag_type (bio.bam.SAMAux attribute) takewhile() (in module ..itertools) tan() (in module ..math) (in module internal.c_stubs) tanh() (in module ..math) (in module internal.c_stubs) Task (class in ..openmp) TaskWithPrivates (class in ..openmp) tau (in module ..math) tee() (in module ..itertools) tell() (internal.file.File method) (internal.file.gzFile method) test() (in module internal.attributes) tgamma() (in module internal.c_stubs) thick_end (bio.bed.BEDRecord attribute) thick_start (bio.bed.BEDRecord attribute) tick() (..time.TimeInterval method) tid (bio.bam.SAMRecord attribute) (bio.locus.Contig attribute) (bio.locus.Locus attribute) tim_sort() (in module algorithms.timsort) tim_sort_array() (in module algorithms.timsort) tim_sort_inplace() (in module algorithms.timsort)

time() (in module ..time) TimeInterval (class in ..time) timing() (in module ..time) title() (internal.str.str method) to_str() (internal.python.pyobj method) tolower() (in module internal.c_stubs) total() (..collections.Counter method) toupper() (in module internal.c_stubs) translate() (bio.pseq.seq method) (in module bio.pseq) (internal.str.str method) triangular() (..random.Random method) (in module ..random) true_score (bio.bwa.mem_alnreg_t attribute) truediv() (in module ..operator) trunc() (in module ..math) (in module internal.c_stubs) truth() (in module ..operator) try_unpack() (in module bio.vcf) TWOPI (in module ..random) type_code (bio.vcf.BCFAux attribute) (bio.vcf.BCFHeaderMetaData attribute) TypeError

U

u16 (in module internal.types.intn) u32 (in module internal.types.intn) u64 (in module internal.types.intn) u8 (in module internal.types.intn) uniform() (..random.Random method) (in module ..random) union() (internal.types.collections.set.Set method) unmapped (bio.bam.SAMRecord attribute)

unpickle() (in module ..pickle) unwrap() (in module internal.types.optional) update() (..collections.Counter method), [1], [2], [3] (bio.fmindex.FMDIndex method) (bio.fmindex.FMIndex method) (internal.types.collections.dict.Dict method) (internal.types.collections.set.Set method) upper() (internal.str.str method)

V

val (bio.vcf.BCFAux attribute) value (bio.vcf.BCFHeaderRecord attribute) VALUE_TYPES (in module bio.vcf) ValueError values() (internal.types.collections.dict.Dict method) variance (..statistics.NormalDist attribute) variance() (in module ..statistics) VCF() (in module bio.vcf)

VCFReader (in module bio.vcf) VCFRecord (class in bio.vcf) VCFRecordFilter (class in bio.vcf) VCFRecordFormat (class in bio.vcf) VCFRecordInfo (class in bio.vcf) VCFRecordSample (class in bio.vcf) VCFRecordSamples (class in bio.vcf) vonmisesvariate() (..random.Random method) (in module ..random)

W

w (bio.bwa.mem_alnreg_t attribute) weibullvariate() (..random.Random method) (in module ..random) whitespace (in module ..string)

with_max() (bio.intervals.Interval method) write() (bio.fasta.FASTAReader method) (internal.file.File method) (internal.file.gzFile method)

X

xor() (in module ..operator)

Z

Z (bio.bam.SAMAux attribute) ZeroDivisionError

zfill() (internal.str.str method) zip() (in module internal.builtin) zip_longest (class in ..itertools)