!_TAG_FILE_FORMAT	2	/extended format; --format=1 will not append ;" to lines/
!_TAG_FILE_SORTED	1	/0=unsorted, 1=sorted, 2=foldcase/
!_TAG_PROGRAM_AUTHOR	Darren Hiebert	/dhiebert@users.sourceforge.net/
!_TAG_PROGRAM_NAME	Exuberant Ctags	//
!_TAG_PROGRAM_URL	http://ctags.sourceforge.net	/official site/
!_TAG_PROGRAM_VERSION	5.8	//
ALN_CIGAR_MAX_LEN	aln_cigar.h	26;"	d
ALN_CIGAR_TYPE_CLIP1	aln_cigar.h	33;"	d
ALN_CIGAR_TYPE_CLIP2	aln_cigar.h	34;"	d
ALN_CIGAR_TYPE_DEL	aln_cigar.h	31;"	d
ALN_CIGAR_TYPE_INS	aln_cigar.h	30;"	d
ALN_CIGAR_TYPE_MAT	aln_cigar.h	29;"	d
ALN_CIGAR_TYPE_NULL	aln_cigar.h	28;"	d
ALN_CIGAR_TYPE_SKIP	aln_cigar.h	32;"	d
ASM_KMER_MASK	asm_R2.h	32;"	d
ASM_KMER_SIZE	asm_R2.h	31;"	d
ASM_R2_H	asm_R2.h	20;"	d
AlnAln	stdaln.h	/^} AlnAln;$/;"	t	typeref:struct:__anon16
AlnCigar	aln_cigar.h	/^} AlnCigar;$/;"	t	typeref:struct:__anon56
AlnParam	stdaln.h	/^} AlnParam;$/;"	t	typeref:struct:__anon14
BaseCnt	divide.c	/^} BaseCnt;$/;"	t	typeref:struct:__anon55	file:
BitVec	bitvec.h	/^} BitVec;$/;"	t	typeref:struct:__anon54
Block	mergetag.c	/^} Block;$/;"	t	typeref:struct:__anon13	file:
BloomFilter	bloom_filter.h	/^} BloomFilter;$/;"	t	typeref:struct:__anon34
BufferedInputFile	file_reader.h	/^} BufferedInputFile;$/;"	t	typeref:struct:__anon33
CC	Makefile	/^CC=gcc$/;"	m
CFLAGS	Makefile	/^CFLAGS= -W -O2 -Wall -finline-functions -D_FILE_OFFSET_BITS=64$/;"	m
C_N_2	divide.c	/^static inline uint32_t C_N_2(uint32_t n){$/;"	f	file:
Cluster	rainbow.h	/^} Cluster;$/;"	t	typeref:struct:__anon20
Ctg	mergecontig.h	/^} Ctg;$/;"	t	typeref:struct:__anon45
CtgDB	mergecontig.h	/^} CtgDB;$/;"	t	typeref:struct:__anon46
D	stdaln.c	/^	int M, I, D;$/;"	m	struct:__anon10	file:
DELETE	ezmsim.c	/^enum muttype_t {NOCHANGE = 0, INSERT = 0x1000, SUBSTITUTE = 0xe000, DELETE = 0xf000};$/;"	e	enum:muttype_t	file:
DEPTH	ezmsim.c	/^static double DEPTH = 10.0;$/;"	v	file:
Div	rainbow.h	/^} Div;$/;"	t	typeref:struct:__anon23
Dt	stdaln.c	/^	unsigned char Mt:3, It:2, Dt:2;$/;"	m	struct:__anon9	file:
EF	asm_R2.h	/^} EF;$/;"	t	typeref:struct:__anon40
EF_main	ezmsim.c	/^int EF_main(int argc, char *argv[])$/;"	f
EF_usage	ezmsim.c	/^int EF_usage()$/;"	f
ERR_RATE	ezmsim.c	/^static double ERR_RATE = 0.02;$/;"	v	file:
FASTA_FLAG_NORMAL	file_reader.h	101;"	d
FASTA_FLAG_NO_NAME	file_reader.h	102;"	d
FASTA_FLAG_NO_SEQ	file_reader.h	103;"	d
FASTQ_FLAG_NORMAL	file_reader.h	109;"	d
FASTQ_FLAG_NO_NAME	file_reader.h	110;"	d
FASTQ_FLAG_NO_QUAL	file_reader.h	112;"	d
FASTQ_FLAG_NO_SEQ	file_reader.h	111;"	d
FContig	asm_R2.h	/^} FContig;$/;"	t	typeref:struct:__anon38
FROM_D	stdaln.h	39;"	d
FROM_I	stdaln.h	38;"	d
FROM_M	stdaln.h	37;"	d
FRead	asm_R2.h	/^} FRead;$/;"	t	typeref:struct:__anon37
FileReader	file_reader.h	/^} FileReader;$/;"	t	typeref:struct:__anon31
GENERIC_SRC	Makefile	/^GENERIC_SRC= string.h bitvec.h file_reader.h hashset.h sort.h list.h dna.h heap.h stdaln.h vector.h$/;"	m
GLIBS	Makefile	/^GLIBS=-lm$/;"	m
Gpush_vec	vector.h	112;"	d
HASH_FLAG_MACROS	hashset.h	53;"	d
HOM_RATE	ezmsim.c	/^static double HOM_RATE = 0.0;$/;"	v	file:
Heap	heap.h	/^} Heap;$/;"	t	typeref:struct:__anon11
I	stdaln.c	/^	int M, I, D;$/;"	m	struct:__anon10	file:
INDEL_EXTEND	ezmsim.c	/^static double INDEL_EXTEND = 0.3;$/;"	v	file:
INDEL_FRAC	ezmsim.c	/^static double INDEL_FRAC = 0.1;$/;"	v	file:
INIT_IDX	ezmsim.c	52;"	d	file:
INIT_SEQ	ezmsim.c	51;"	d	file:
INSERT	ezmsim.c	/^enum muttype_t {NOCHANGE = 0, INSERT = 0x1000, SUBSTITUTE = 0xe000, DELETE = 0xf000};$/;"	e	enum:muttype_t	file:
It	stdaln.c	/^	unsigned char Mt:3, It:2, Dt:2;$/;"	m	struct:__anon9	file:
KMER_NUM	rainbow.h	/^	uint32_t KMER_NUM;$/;"	m	struct:__anon20
KMER_SIZE	rainbow.h	/^	uint32_t KMER_SIZE;$/;"	m	struct:__anon20
KMER_SIZE_CTG	mergecontig.h	13;"	d
K_allele	rainbow.h	/^	uint32_t k_allele, K_allele;$/;"	m	struct:__anon23
LH3_STDALN_H_	stdaln.h	24;"	d
LOCAL_OVERFLOW_REDUCE	stdaln.c	233;"	d	file:
LOCAL_OVERFLOW_THRESHOLD	stdaln.c	232;"	d	file:
LR_main	ezmsim.c	/^int LR_main(int argc, char *argv[])$/;"	f
LR_usage	ezmsim.c	/^int LR_usage() {$/;"	f
M	stdaln.c	/^	int M, I, D;$/;"	m	struct:__anon10	file:
MAX_RD_LEN	asm_R2.h	30;"	d
MERGECTG_H	mergectg.h	2;"	d
MINOR_INF	stdaln.h	42;"	d
MUT_RATE	ezmsim.c	/^static double MUT_RATE = 0.001;$/;"	v	file:
MYALLOC	stdaln.h	31;"	d
MYFREE	stdaln.h	34;"	d
Mt	stdaln.c	/^	unsigned char Mt:3, It:2, Dt:2;$/;"	m	struct:__anon9	file:
MurmurHash64A	hashset.h	/^static inline uint64_t MurmurHash64A(const void * key, int len, uint32_t seed){$/;"	f
NOCHANGE	ezmsim.c	/^enum muttype_t {NOCHANGE = 0, INSERT = 0x1000, SUBSTITUTE = 0xe000, DELETE = 0xf000};$/;"	e	enum:muttype_t	file:
NT_LOCAL_MASK	stdaln.c	236;"	d	file:
NT_LOCAL_SCORE	stdaln.c	234;"	d	file:
NT_LOCAL_SHIFT	stdaln.c	235;"	d	file:
ONES_STEP_4	bitvec.h	92;"	d
ONES_STEP_8	bitvec.h	93;"	d
Overlap	asm_R2.h	/^} Overlap;$/;"	t	typeref:struct:__anon39
PACKAGE_VERSION	ezmsim.c	11;"	d	file:
PWDB	mergecontig.h	/^} PWDB;$/;"	t	typeref:struct:__anon48
PWcontig	mergecontig.h	/^} PWcontig;$/;"	t	typeref:struct:__anon47
RD_KMER_SIZE	mergectg.h	/^	uint32_t RD_KMER_SIZE; \/\/ parameter$/;"	m	struct:__anon8
REC	mergetag.c	/^} REC;$/;"	t	typeref:struct:__anon12	file:
ReadInfo	rainbow.h	/^} ReadInfo;$/;"	t	typeref:struct:__anon21
SBT	rainbow.h	/^} SBT;$/;"	t	typeref:struct:__anon19
SEQ_BLOCK_SIZE	ezmsim.c	/^static int SEQ_BLOCK_SIZE = 512;$/;"	v	file:
SET_INF	stdaln.c	238;"	d	file:
STDALN_VERSION	stdaln.h	27;"	d
SUBSTITUTE	ezmsim.c	/^enum muttype_t {NOCHANGE = 0, INSERT = 0x1000, SUBSTITUTE = 0xe000, DELETE = 0xf000};$/;"	e	enum:muttype_t	file:
SWAP_TMP	string.h	34;"	d
SeqDB	rainbow.h	/^} SeqDB;$/;"	t	typeref:struct:__anon18
SeqFileAttr	file_reader.h	/^} SeqFileAttr;$/;"	t	typeref:struct:__anon32
Sequence	file_reader.h	/^} Sequence;$/;"	t	typeref:struct:__anon29
SimpAssembler	simp_asm.h	/^} SimpAssembler;$/;"	t	typeref:struct:__anon51
SimpContigInfo	simp_asm.h	/^} SimpContigInfo;$/;"	t	typeref:struct:__anon50
SimpSeqInfo	simp_asm.h	/^} SimpSeqInfo;$/;"	t	typeref:struct:__anon49
String	string.h	/^} String;$/;"	t	typeref:struct:__anon52
Vector	vector.h	/^typedef struct Vector {$/;"	s
Vector	vector.h	/^} Vector;$/;"	t	typeref:struct:Vector
VirtualString	string.h	/^} VirtualString;$/;"	t	typeref:struct:__anon53
__ALN_CIGAR_RJ_H	aln_cigar.h	21;"	d
__BIT_VEC_RJ_H	bitvec.h	21;"	d
__BLOOM_FILTER_RJ_H	bloom_filter.h	22;"	d
__DNA_RJ_H	dna.h	21;"	d
__FILE_READER_RJ_H	file_reader.h	21;"	d
__HASH_SET_RJ	hashset.h	21;"	d
__HEAP_RJ_H	heap.h	21;"	d
__LIST_RJ_H	list.h	21;"	d
__MERGECONTIG_H	mergecontig.h	2;"	d
__RAINBOW_RJ_H	rainbow.h	21;"	d
__SIMPLE_ASM_RJ_H	simp_asm.h	21;"	d
__SORT_RJ_H	sort.h	21;"	d
__STRING_RJ_H	string.h	21;"	d
__VECTOR_H_RJ	vector.h	21;"	d
__lh3_Jenkins_hash_64	hashset.h	/^static inline uint64_t __lh3_Jenkins_hash_64(uint64_t key){$/;"	f
__lh3_Jenkins_hash_int	hashset.h	/^static inline uint32_t __lh3_Jenkins_hash_int(uint32_t key){$/;"	f
__string_hashcode	hashset.h	/^static inline uint32_t __string_hashcode(const char *s){$/;"	f
_aln_cigar_add_cigar	aln_cigar.h	/^static inline int _aln_cigar_add_cigar(AlnCigar *cs, int n_cigar, int len, int type){$/;"	f
_aln_cigar_h_num_str_len	aln_cigar.h	/^static inline int _aln_cigar_h_num_str_len(int n){$/;"	f
_call_key_col	divide.c	/^uint32_t _call_key_col(Div *div, uint32_t gid){$/;"	f
_rj_hashset_find_prime	hashset.h	/^static inline uint64_t _rj_hashset_find_prime(uint64_t n){$/;"	f
add_char_string	string.h	/^static inline void add_char_string(String *str, char ch){$/;"	f
add_hashset_macro	hashset.h	172;"	d
add_read2ef	asm_R2.c	/^void add_read2ef(EF *ef, char *seq, uint32_t seq_id, uint32_t rd_len, uint32_t rank){ add_read2ef_core(ef, seq, seq_id, rd_len, (rank == 0)? 1 : rank); }$/;"	f
add_read2ef_core	asm_R2.c	/^void add_read2ef_core(EF *ef, char *seq, uint32_t seq_id, uint32_t rd_len, uint32_t rank){$/;"	f
add_vec_size	vector.h	/^static inline int add_vec_size(Vector *vec, size_t add_size){$/;"	f
align_reads_ef	asm_R2.c	/^void align_reads_ef(EF *ef){$/;"	f
aln_aa_rev_table	stdaln.c	/^char *aln_aa_rev_table = "ARNDCQEGHILKMFPSTWYV*X-";$/;"	v
aln_aa_table	stdaln.c	/^unsigned char aln_aa_table[256] = {$/;"	v
aln_cigar_string	aln_cigar.h	/^static const char aln_cigar_string[8] = "?IDM?SHN";$/;"	v
aln_cmp	mergecontig.c	/^int aln_cmp(const void *p0, const void *p1, void *ref) {$/;"	f
aln_ext_size	simp_asm.h	/^	int      aln_ext_size;$/;"	m	struct:__anon51
aln_free_AlnAln	stdaln.c	/^void aln_free_AlnAln(AlnAln *aa)$/;"	f
aln_global_core	stdaln.c	/^int aln_global_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,$/;"	f
aln_init_AlnAln	stdaln.c	/^AlnAln *aln_init_AlnAln()$/;"	f
aln_init_score_array	stdaln.c	/^void aln_init_score_array(unsigned char *seq, int len, int row, int *score_matrix, int **s_array)$/;"	f
aln_local_core	stdaln.c	/^int aln_local_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,$/;"	f
aln_nt16_rev_table	stdaln.c	/^char *aln_nt16_rev_table = "XAGRCMSVTWKDYHBN-";$/;"	v
aln_nt16_table	mergecontig.h	/^static unsigned char aln_nt16_table[256] = {$/;"	v
aln_nt16_table	stdaln.c	/^unsigned char aln_nt16_table[256] = {$/;"	v
aln_nt4_rev_table	stdaln.c	/^char *aln_nt4_rev_table = "AGCTN-";$/;"	v
aln_nt4_table	stdaln.c	/^unsigned char aln_nt4_table[256] = {$/;"	v
aln_param_aa2aa	stdaln.c	/^AlnParam aln_param_aa2aa   = { 12,  2,  2, aln_sm_blosum62, 22, 50 };$/;"	v
aln_param_nt2nt	stdaln.c	/^AlnParam aln_param_nt2nt   = { 10,  2,  2, aln_sm_nt, 16, 75 };$/;"	v
aln_param_rd2rd	stdaln.c	/^AlnParam aln_param_rd2rd   = { 20, 19, 19, aln_sm_read, 16, 75 };$/;"	v
aln_sm_blosum45	stdaln.c	/^int aln_sm_blosum45[] = {$/;"	v
aln_sm_blosum62	stdaln.c	/^int aln_sm_blosum62[] = {$/;"	v
aln_sm_hs	stdaln.c	/^int aln_sm_hs[] = {$/;"	v
aln_sm_nt	stdaln.c	/^int aln_sm_nt[] = {$/;"	v
aln_sm_read	stdaln.c	/^int aln_sm_read[] = {$/;"	v
aln_stdaln	stdaln.c	/^AlnAln *aln_stdaln(const char *seq1, const char *seq2, const AlnParam *ap, int is_global, int do_align)$/;"	f
aln_stdaln_aux	stdaln.c	/^AlnAln *aln_stdaln_aux(const char *seq1, const char *seq2, const AlnParam *ap,$/;"	f
aln_str	mergecontig.h	/^static inline void aln_str(char *s1, char *s2, int *mm, int *mn, int *score) {$/;"	f
aln_trans_table_eu	stdaln.c	/^unsigned char aln_trans_table_eu[66] = {$/;"	v
aln_trans_table_eu_char	stdaln.c	/^char *aln_trans_table_eu_char = "KKNNRRSSTTTTIMIIEEDDGGGGAAAAVVVVQQHHRRRRPPPPLLLL**YY*WCCSSSSLLFFX";$/;"	v
alning_core	cluster.c	/^uint32_t alning_core(Cluster *cluster){$/;"	f
ap	simp_asm.h	/^	AlnParam ap;$/;"	m	struct:__anon51
append_cigars	aln_cigar.h	/^static inline int append_cigars(AlnCigar *cs, int n, int type, int len){$/;"	f
append_string	string.h	/^static inline void append_string(String *str, char *src, int offlen){$/;"	f
apply_array	sort.h	92;"	d
apply_cigars	aln_cigar.h	/^static inline int apply_cigars(AlnCigar *dst, AlnCigar *c1, int n1, AlnCigar *c2, int n2){$/;"	f
as_string	string.h	/^static inline String* as_string(char *chs){$/;"	f
asm_ef	asm_R2.c	/^uint32_t asm_ef(FileReader *in, FILE *out, uint32_t min_ol, float min_sm, uint32_t min_read, uint32_t max_read){$/;"	f
asm_ef_ctgs	asm_R2.c	/^void asm_ef_ctgs(EF *ef){$/;"	f
avg_seq_len	file_reader.h	/^	int avg_seq_len;$/;"	m	struct:__anon32
band_width	stdaln.h	/^	int band_width;$/;"	m	struct:__anon14
base	divide.c	/^	uint32_t base;$/;"	m	struct:__anon55	file:
base	rainbow.h	/^	uint32_t col, cnt, base;$/;"	m	struct:__anon22
base_bit4_table	dna.h	/^static const uint8_t base_bit4_table[256] = {$/;"	v
base_bit_table	dna.h	/^static const uint8_t base_bit_table[256] = {$/;"	v
beg_seq2kmers	dna.h	107;"	d
beg_seq2revkmers	dna.h	114;"	d
begin_iter_bitvec	bitvec.h	/^static inline void begin_iter_bitvec(BitVec *bitv){ bitv->iter_idx = 0; }$/;"	f
begin_iter_simpasm	simp_asm.h	/^static inline void begin_iter_simpasm(SimpAssembler *sa){ sa->iter_idx = 0; }$/;"	f
bit2bits	dna.h	144;"	d
bit4_base_table	dna.h	/^static const char bit4_base_table[16] = "-ACMGRSVTWYHKDBN";$/;"	v
bit4_bit_table	dna.h	/^static const uint8_t bit4_bit_table[16] = { 4, 0, 1, 4,  2, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4 };$/;"	v
bit_base_table	dna.h	/^static const char bit_base_table[6] = "ACGTN-";$/;"	v
bits	bitvec.h	/^	uint64_t *bits;$/;"	m	struct:__anon54
bits	bloom_filter.h	/^	BitVec *bits;$/;"	m	struct:__anon34
bits2bit	dna.h	165;"	d
bits2revseq	dna.h	/^static inline void bits2revseq(char *seq, uint64_t *bits, uint64_t off, uint32_t len){$/;"	f
bits2seq	dna.h	/^static inline void bits2seq(char *seq, uint64_t *bits, uint64_t off, uint32_t len){$/;"	f
bloom_filter_total_seeds	bloom_filter.h	/^static const uint32_t bloom_filter_total_seeds = 20;$/;"	v
bsearch_vec	vector.h	/^static inline void* bsearch_vec(Vector *vec, void *q, cmp_vec_fun fun){$/;"	f
bt	rainbow.h	/^	uint32_t bt;$/;"	m	struct:__anon19
bts	rainbow.h	/^	u32list *bts;$/;"	m	struct:__anon20
buf_cap	file_reader.h	/^	int buf_off, buf_size, buf_cap;$/;"	m	struct:__anon33
buf_off	file_reader.h	/^	int buf_off, buf_size, buf_cap;$/;"	m	struct:__anon33
buf_size	file_reader.h	/^	int buf_off, buf_size, buf_cap;$/;"	m	struct:__anon33
buffer	file_reader.h	/^	char *buffer;$/;"	m	struct:__anon31
buffer	file_reader.h	/^	void *buffer;$/;"	m	struct:__anon33
buffer	vector.h	/^	void *buffer;$/;"	m	struct:Vector
build_tree	mergectg.c	/^void build_tree(merge_t *merger) {$/;"	f
cache	mergectg.h	/^	contigsv *cache;$/;"	m	struct:__anon8
cache	rainbow.h	/^	u32slist *grps, *cache;$/;"	m	struct:__anon23
cal_2seq_mm_core	cluster.c	/^uint8_t cal_2seq_mm_core(uint64_t *seq1, uint64_t *seq2, uint8_t len1, uint8_t len2){$/;"	f
cal_mm	mergetag.c	/^uint32_t cal_mm(String *seqs, Block *b1, Block *b2){$/;"	f
call_key_col	divide.c	/^uint32_t call_key_col(Div *div, uint32_t gid){$/;"	f
cap	vector.h	/^	size_t cap;$/;"	m	struct:Vector
capacity	file_reader.h	/^	int capacity;$/;"	m	struct:__anon31
capacity	string.h	/^	int capacity;$/;"	m	struct:__anon52
cat_cigars	aln_cigar.h	/^static inline int cat_cigars(AlnCigar *cigars1, int n_cigar1, AlnCigar *cigars2, int n_cigar2){$/;"	f
cat_vec	vector.h	/^static inline int cat_vec(Vector *dst, Vector *src){$/;"	f
catstr	string.h	/^static inline char* catstr(int n_str, ...){$/;"	f
cbs	rainbow.h	/^	cbv *cbs;$/;"	m	struct:__anon23
change_seeds_bloomfilter	bloom_filter.h	/^static inline void change_seeds_bloomfilter(BloomFilter *bf){ bf->seed_off = (bf->seed_off + bf->n_seed) % bloom_filter_total_seeds; }$/;"	f
chash_code	hashset.h	499;"	d
chash_equals	hashset.h	500;"	d
chomp_string	string.h	/^static inline void chomp_string(String *str){$/;"	f
cid	mergectg.h	/^	uint32_t cid; \/\/$/;"	m	struct:__anon8
cid	mergetag.c	/^	uint32_t rid, cid, gid, rank, off1, len1, off2, len2;$/;"	m	struct:__anon12	file:
cigars2string	aln_cigar.h	/^static inline char* cigars2string(AlnCigar *cigars, int n_cigar, char *str){$/;"	f
cigars_lengths	aln_cigar.h	/^static inline void cigars_lengths(AlnCigar *cigars, int n_cigar, int *aln_size, int *seq1_size, int *seq2_size){$/;"	f
cigars_seq2aln	aln_cigar.h	/^static inline int cigars_seq2aln(char *dst, AlnCigar *c, int n, int seq_idx, char *seq){$/;"	f
clear_bitvec	bitvec.h	/^static inline void clear_bitvec(BitVec *bitv){ bitv->n_bit = 0; }$/;"	f
clear_bloomfilter	bloom_filter.h	/^static inline void clear_bloomfilter(BloomFilter *bf){ zeros_bitvec(bf->bits); }$/;"	f
clear_ctg	mergectg.c	/^void clear_ctg(contig_t *ctg) {$/;"	f
clear_entity_del	hashset.h	60;"	d
clear_entity_null	hashset.h	59;"	d
clear_hashset_macro	hashset.h	265;"	d
clear_heap	heap.h	/^static inline void clear_heap(Heap *heap){ clear_rjheapv(heap->ptrs); }$/;"	f
clear_string	string.h	/^static inline void clear_string(String *str){ str->size = 0; }$/;"	f
clear_vec	vector.h	217;"	d
clone_string	string.h	/^static inline String* clone_string(String *str){ $/;"	f
close_bif	file_reader.h	/^static inline void close_bif(BufferedInputFile *bif){$/;"	f
closed	asm_R2.h	/^	uint32_t len:31, closed:1;$/;"	m	struct:__anon38
closed	mergectg.h	/^	int closed;$/;"	m	struct:__anon3
closed	simp_asm.h	/^	uint32_t len:31, closed:1;$/;"	m	struct:__anon50
cls_id	mergecontig.h	/^	uint32_t cls_id;$/;"	m	struct:__anon45
cluster_invoker	main.c	/^int cluster_invoker(int argc, char **argv){$/;"	f
clustering	cluster.c	/^void clustering(Cluster *cluster, FileReader *fr2, int is_fq2, int fix_rd_len, FILE *out){$/;"	f
clustering_ctg	mergecontig.c	/^PWDB* clustering_ctg(PWDB *db, uint32_t min_overlap, float het) {$/;"	f
cmp	heap.h	/^	heap_comp_func cmp;$/;"	m	struct:__anon11
cmp_2nums_proc	sort.h	26;"	d
cmp_ctg_clsid	mergecontig.c	/^int cmp_ctg_clsid(const void *p0, const void *p1) {$/;"	f
cmp_ids	mergecontig.h	/^static inline int cmp_ids(const void *e1, const void *e2) {$/;"	f
cmp_kmer_pos	mergecontig.h	/^static inline int cmp_kmer_pos (const void *e1, const void *e2) {$/;"	f
cmp_ol_func	asm_R2.c	/^int cmp_ol_func(const void *e1, const void *e2){$/;"	f
cmp_sbt	cluster.c	/^inline int cmp_sbt(const void *e1, const void *e2){$/;"	f
cmp_sr_alnhit	simp_asm.h	/^static inline int cmp_sr_alnhit(const void *e1, const void *e2){$/;"	f
cmp_vec_fun	vector.h	/^typedef int (*cmp_vec_fun)(const void *k1, const void *k2);$/;"	t
cns_len	mergetag.c	/^	uint32_t cns_off, cns_len;$/;"	m	struct:__anon13	file:
cns_off	mergetag.c	/^	uint32_t cns_off, cns_len;$/;"	m	struct:__anon13	file:
cnt	divide.c	/^	uint32_t cnt;$/;"	m	struct:__anon55	file:
cnt	rainbow.h	/^	uint32_t col, cnt, base;$/;"	m	struct:__anon22
col	rainbow.h	/^	uint32_t col, cnt, base;$/;"	m	struct:__anon22
col_base_t	rainbow.h	/^} col_base_t;$/;"	t	typeref:struct:__anon22
comment	file_reader.h	/^	String comment;$/;"	m	struct:__anon29
compile_cigars	aln_cigar.h	/^static inline int compile_cigars(AlnCigar *dst, AlnCigar *c1, int n1, AlnCigar *c2, int n2, int seq_idx){$/;"	f
consensus	mergetag.c	/^void consensus(recv *divs, String *seqs, uint32_t beg, uint32_t end, uint32_t *cns_off, uint32_t *cns_len){$/;"	f
contig_code	mergectg.h	46;"	d
contig_eq	mergectg.h	47;"	d
contig_seq_t	mergectg.h	/^} contig_seq_t;$/;"	t	typeref:struct:__anon4
contig_t	mergectg.h	/^} contig_t; $/;"	t	typeref:struct:__anon3
count_hashset_macro	hashset.h	263;"	d
count_heap	heap.h	/^static inline size_t count_heap(Heap *heap){ return count_rjheapv(heap->ptrs); }$/;"	f
count_ones_bit32	bitvec.h	/^static inline uint32_t count_ones_bit32(uint32_t v){$/;"	f
count_ones_bit64	bitvec.h	/^static inline int count_ones_bit64(const uint64_t x){$/;"	f
ctg_dir	simp_asm.h	/^	uint32_t ctg_id, ctg_dir:1, ctg_off:20, used:1, rank:10;$/;"	m	struct:__anon49
ctg_id	asm_R2.h	/^	uint32_t ctg_id:24, ctg_off:19, used:1;$/;"	m	struct:__anon37
ctg_id	simp_asm.h	/^	uint32_t ctg_id, ctg_dir:1, ctg_off:20, used:1, rank:10;$/;"	m	struct:__anon49
ctg_kmer_t	mergectg.h	/^} ctg_kmer_t;$/;"	t	typeref:struct:__anon5
ctg_off	asm_R2.h	/^	uint32_t ctg_id:24, ctg_off:19, used:1;$/;"	m	struct:__anon37
ctg_off	simp_asm.h	/^	uint32_t ctg_id, ctg_dir:1, ctg_off:20, used:1, rank:10;$/;"	m	struct:__anon49
ctgnum	mergecontig.h	/^	uint32_t ctgnum;$/;"	m	struct:__anon46
ctgs	asm_R2.h	/^	Vector   *ctgs;$/;"	m	struct:__anon40
ctgs	mergecontig.h	/^	ctglist *ctgs;$/;"	m	struct:__anon46
ctgs	mergectg.h	/^	contigv *ctgs;$/;"	m	struct:__anon8
ctgs	simp_asm.h	/^	ctgv     *ctgs;$/;"	m	struct:__anon51
ctgv	mergecontig.h	/^	ctglist *ctgv;$/;"	m	struct:__anon48
ctype	stdaln.h	/^	unsigned char ctype;$/;"	m	struct:__anon15
cuhash_code	hashset.h	509;"	d
cuhash_equals	hashset.h	510;"	d
cuhash_t	hashset.h	/^typedef struct { char *key; uint32_t val; } cuhash_t;$/;"	t	typeref:struct:__anon28
define_apply_array	sort.h	230;"	d
define_bubble_sort	sort.h	29;"	d
define_hashset	hashset.h	371;"	d
define_list	list.h	214;"	d
define_list_core	list.h	39;"	d
define_list_ext	list.h	166;"	d
define_merge	sort.h	153;"	d
define_native_list	list.h	218;"	d
define_quick_sort	sort.h	114;"	d
define_reverse_array	sort.h	217;"	d
define_revsere_vec	vector.h	177;"	d
define_search_array	sort.h	241;"	d
define_unique_merge	sort.h	202;"	d
delimiter	file_reader.h	/^	char delimiter;$/;"	m	struct:__anon31
deps	rainbow.h	/^	u32list *deps;$/;"	m	struct:__anon23
destroy_tree	mergectg.c	/^void destroy_tree(pathtree_t *t) {$/;"	f
div_invoker	main.c	/^int div_invoker(int argc, char **argv){$/;"	f
div_reads	divide.c	/^uint32_t div_reads(Div *div, FileReader *fr, FILE *out){$/;"	f
dividing	divide.c	/^void dividing(Div *div, uint32_t old_gid, FILE *out){$/;"	f
dividing_core	divide.c	/^void dividing_core(Div *div, uint32_t gid, int dep){$/;"	f
dna_rev_seq	dna.h	/^static inline uint64_t dna_rev_seq(uint64_t seq, uint8_t seq_size){$/;"	f
dna_xor2ones	dna.h	/^static inline uint64_t dna_xor2ones(uint64_t seq){$/;"	f
dpcell_t	stdaln.c	/^} dpcell_t;$/;"	t	typeref:struct:__anon9	file:
dpscore_t	stdaln.c	/^} dpscore_t;$/;"	t	typeref:struct:__anon10	file:
dump_hashset_macro	hashset.h	277;"	d
dump_vec	vector.h	/^static inline size_t dump_vec(Vector *vec, FILE *out){$/;"	f
e_size	vector.h	/^	unsigned int e_size;$/;"	m	struct:Vector
ef	mergectg.h	/^	EF *ef;$/;"	m	struct:__anon8
ef_id	asm_R2.h	/^	uint32_t ef_id;$/;"	m	struct:__anon40
ef_usage	asm_R2.c	/^int ef_usage(){$/;"	f
encap_bitvec	bitvec.h	/^static inline void encap_bitvec(BitVec *bitv, uint64_t num){$/;"	f
encap_hashset_macro	hashset.h	317;"	d
encap_vec	vector.h	/^static inline int encap_vec(Vector *vec, unsigned int add_size){$/;"	f
end1	stdaln.h	/^	int start1, end1; \/* start and end of the first sequence, coordinations are 1-based *\/$/;"	m	struct:__anon16
end2	stdaln.h	/^	int start2, end2; \/* start and end of the second sequence, coordinations are 1-based *\/$/;"	m	struct:__anon16
end_seq2kmers	dna.h	112;"	d
end_seq2kmers	dna.h	119;"	d
err_xopen_core	ezmsim.c	/^FILE *err_xopen_core(const char *func, const char *fn, const char *mode)$/;"	f
eseq	asm_R2.h	/^	char     eseq[MAX_RD_LEN];$/;"	m	struct:__anon40
exact_limit	rainbow.h	/^	uint32_t exact_limit;$/;"	m	struct:__anon20
execute_pwaln	mergecontig.c	/^void execute_pwaln(CtgDB *db, uint32_t min_overlap, float het, uint32_t max_nctg) {$/;"	f
exists_entity	hashset.h	56;"	d
exists_hashset_macro	hashset.h	153;"	d
ezmsim_EF_core	ezmsim.c	/^void ezmsim_EF_core(FILE *fpout1, FILE *fpout2, FILE *fp_fa, unsigned int size_l, unsigned int size_r, unsigned char *cut, int pos, int distance, int ovlp, int stp, int reverse, int is_hap)$/;"	f
ezmsim_LR_core	ezmsim.c	/^void ezmsim_LR_core(FILE *fpout1, FILE *fpout2, FILE *fp_fa, int size_l, int size_r, unsigned char *cut, int pos)$/;"	f
fclose_filereader	file_reader.c	/^void fclose_filereader(FileReader *fr){$/;"	f
ffread	hashset.h	275;"	d
ffwrite	hashset.h	274;"	d
fidx	file_reader.h	/^	uint32_t fidx;$/;"	m	struct:__anon31
file	file_reader.h	/^	FILE *file;$/;"	m	struct:__anon30
file	file_reader.h	/^	FILE *file;$/;"	m	struct:__anon33
filename	file_reader.h	/^	char *filename;$/;"	m	struct:__anon30
files	file_reader.h	/^	Vector *files;$/;"	m	struct:__anon31
find_overlap	asm_R2.c	/^void find_overlap(char *seq1, uint32_t len1, uint32_t off1, char *seq2, uint32_t len2, uint32_t off2, uint32_t *l_ol, uint32_t *r_ol, uint32_t *n_mm){$/;"	f
flag	mergectg.h	/^	int flag;  \/\/ if == 0 first use, init; else reset$/;"	m	struct:__anon8
flags	rainbow.h	/^	BitVec  *flags;$/;"	m	struct:__anon20
flip_bitvec	bitvec.h	/^static inline void flip_bitvec(BitVec *bitv, uint64_t idx){ bitv->bits[idx>>6] ^= 1LLU << (idx&0x3FU); }$/;"	f
flip_cigars	aln_cigar.h	/^static inline void flip_cigars(AlnCigar *cigars, int n_cigar){$/;"	f
fopen_filereader	file_reader.c	/^FileReader* fopen_filereader(char *filename){$/;"	f
fopen_filereader2	file_reader.c	/^FileReader* fopen_filereader2(char *prefix, char *postfix){$/;"	f
fopen_m_filereader	file_reader.c	/^FileReader* fopen_m_filereader(int n_file, char **filenames){$/;"	f
fr_file_t	file_reader.h	/^} fr_file_t;$/;"	t	typeref:struct:__anon30
fr_fread	file_reader.c	/^static inline int fr_fread(void *buf, size_t e_size, size_t size, FILE *in){$/;"	f	file:
fread_all	file_reader.c	/^char *fread_all(FileReader *fr){$/;"	f
fread_fasta	file_reader.h	107;"	d
fread_fasta_adv	file_reader.c	/^int fread_fasta_adv(Sequence **seq_ptr, FileReader *fr, int fasta_flag){$/;"	f
fread_fastq	file_reader.h	116;"	d
fread_fastq_adv	file_reader.c	/^int fread_fastq_adv(Sequence **seq_ptr, FileReader *fr, int fastq_flag){$/;"	f
fread_line	file_reader.c	/^int fread_line(String *line, FileReader *fr){$/;"	f
fread_line2	file_reader.c	/^int fread_line2(String *line, FileReader *fr){$/;"	f
fread_table	file_reader.c	/^int fread_table(FileReader *fr){$/;"	f
free_bitvec	bitvec.h	/^static inline void free_bitvec(BitVec *bitv){$/;"	f
free_bloomfilter	bloom_filter.h	/^static inline void free_bloomfilter(BloomFilter *bf){$/;"	f
free_cluster	cluster.c	/^void free_cluster(Cluster *cluster){$/;"	f
free_ctg	mergectg.c	/^void free_ctg(contig_t *ctg) {$/;"	f
free_ctgdb	mergecontig.c	/^void free_ctgdb(CtgDB *db) {$/;"	f
free_ctgs	mergectg.c	/^void free_ctgs(merge_t *merger) {$/;"	f
free_div	divide.c	/^void free_div(Div *div){$/;"	f
free_ef	asm_R2.c	/^void free_ef(EF *ef){$/;"	f
free_hashset_macro	hashset.h	310;"	d
free_heap	heap.h	/^static inline void free_heap(Heap *heap){ free_rjheapv(heap->ptrs); free(heap); }$/;"	f
free_load_ctgdb	mergecontig.c	/^void free_load_ctgdb(CtgDB *db) {$/;"	f
free_merger	mergectg.c	/^void free_merger(merge_t *merger) {$/;"	f
free_pwdb	mergecontig.c	/^void free_pwdb(PWDB *db) {$/;"	f
free_sequence	file_reader.h	59;"	d
free_simpasm	simp_asm.h	/^static inline void free_simpasm(SimpAssembler *sa){$/;"	f
free_string	string.h	/^static inline void free_string(String *str){ free(str->string); free(str); }$/;"	f
free_tree	mergectg.c	/^void free_tree(merge_t *merger) {$/;"	f
free_vec	vector.h	/^static inline void free_vec(Vector *vec){$/;"	f
froll_back	file_reader.c	/^int froll_back(FileReader *fr){$/;"	f
gap_end	stdaln.h	/^	int gap_end;$/;"	m	struct:__anon14
gap_ext	stdaln.h	/^	int gap_ext;$/;"	m	struct:__anon14
gap_open	stdaln.h	/^	int gap_open;$/;"	m	struct:__anon14
get_2bit16	bitvec.h	33;"	d
get_2bit32	bitvec.h	34;"	d
get_2bit64	bitvec.h	35;"	d
get_2bit8	bitvec.h	32;"	d
get_bit16	bitvec.h	28;"	d
get_bit32	bitvec.h	29;"	d
get_bit64	bitvec.h	30;"	d
get_bit8	bitvec.h	27;"	d
get_bitvec	bitvec.h	/^static inline uint64_t get_bitvec(BitVec *bitv, uint64_t idx){ return (bitv->bits[idx>>6] >> (idx&0x3FU)) & 0x01LLU; }$/;"	f
get_bloomfilter	bloom_filter.h	/^static inline int  get_bloomfilter(BloomFilter *bf, const void *key, uint32_t len){$/;"	f
get_col_len	file_reader.h	89;"	d
get_col_str	file_reader.h	88;"	d
get_col_vstr	file_reader.h	87;"	d
get_hashset_macro	hashset.h	94;"	d
get_last_vec_ref	vector.h	/^static inline void* get_last_vec_ref(Vector *vec){$/;"	f
get_next_vec_ref	vector.h	/^static inline void* get_next_vec_ref(Vector *vec){$/;"	f
get_pool_ctg	asm_R2.c	/^FContig* get_pool_ctg(EF *ef){$/;"	f
get_pool_vec	asm_R2.c	/^Vector* get_pool_vec(EF *ef){$/;"	f
get_vec	vector.h	/^static inline int get_vec(Vector *vec, size_t idx, void *e){$/;"	f
get_vec_ref	vector.h	/^static inline void* get_vec_ref(Vector *vec, size_t idx){$/;"	f
gget_vec	vector.h	133;"	d
gid	mergetag.c	/^	uint32_t gid, off, len;$/;"	m	struct:__anon13	file:
gid	mergetag.c	/^	uint32_t rid, cid, gid, rank, off1, len1, off2, len2;$/;"	m	struct:__anon12	file:
gid_map	rainbow.h	/^	u32list *gid_map;$/;"	m	struct:__anon20
gidoff	rainbow.h	/^	uint32_t gidoff;$/;"	m	struct:__anon20
gidoff	rainbow.h	/^	uint32_t gidoff;$/;"	m	struct:__anon23
gids	rainbow.h	/^	u32list *gids;$/;"	m	struct:__anon20
gids	rainbow.h	/^	u32list *gids;$/;"	m	struct:__anon23
gpeer_vec	vector.h	139;"	d
gpop_vec	vector.h	120;"	d
gpush_vec	vector.h	111;"	d
grps	rainbow.h	/^	u32slist *grps, *cache;$/;"	m	struct:__anon23
gset_vec	vector.h	126;"	d
guess_seq_file	file_reader.c	/^void guess_seq_file(FileReader *fr, SeqFileAttr *attr){$/;"	f
guess_seq_file_type	file_reader.c	/^int guess_seq_file_type(FileReader *fr){$/;"	f
hash64shift	hashset.h	/^static inline uint64_t hash64shift(uint64_t key){$/;"	f
heap_comp_func	heap.h	/^typedef int (*heap_comp_func)(const void *e1, const void *e2, void *ref);$/;"	t
het	mergecontig.h	/^	float het;$/;"	m	struct:__anon47
het	mergectg.h	/^	float het; \/\/ parameter$/;"	m	struct:__anon8
hp	mergecontig.h	/^	Heap *hp;$/;"	m	struct:__anon48
i	stdaln.h	/^	int i, j;$/;"	m	struct:__anon15
i32hash_code	hashset.h	495;"	d
i32hash_equals	hashset.h	496;"	d
id	mergecontig.h	/^	uint32_t id;$/;"	m	struct:__anon43
id	mergecontig.h	/^	uint32_t id;$/;"	m	struct:__anon45
id	mergectg.h	/^	uint32_t id; \/\/ which contig$/;"	m	struct:__anon5
id	mergectg.h	/^	uint32_t id;$/;"	m	struct:__anon3
id	mergectg.h	/^	uint32_t id;$/;"	m	struct:__anon4
id0	mergecontig.h	/^	uint32_t id0;$/;"	m	struct:__anon47
id1	mergecontig.h	/^	uint32_t id1;$/;"	m	struct:__anon47
id_tt	mergecontig.h	/^} id_tt;$/;"	t	typeref:struct:__anon43
idx	ezmsim.c	/^	uint64_t *idx;$/;"	m	struct:__anon26	file:
idx_t	ezmsim.c	/^} idx_t;$/;"	t	typeref:struct:__anon26	file:
idxs	rainbow.h	/^	uint32_t idxs[2];$/;"	m	struct:__anon20
inc_tag	asm_R2.h	/^	uint32_t inc_tag;$/;"	m	struct:__anon40
index	asm_R2.h	/^	rhash    *index;$/;"	m	struct:__anon40
index	mergectg.h	/^	rdkhash *index;$/;"	m	struct:__anon3
index	rainbow.h	/^	khash *index;$/;"	m	struct:__anon20
index_bitvec	bitvec.h	/^static inline void index_bitvec(BitVec *bitv){$/;"	f
index_rds	mergectg.c	/^void index_rds(merge_t *merger, contig_t *ctg) {$/;"	f
indexing_cluster	cluster.c	/^void indexing_cluster(Cluster *cluster, FileReader *fr, int is_fq, int fix_rd_len){$/;"	f
init_bif	file_reader.h	/^static inline BufferedInputFile* init_bif(FILE *file, int buf_size){$/;"	f
init_bitvec	bitvec.h	/^static inline BitVec* init_bitvec(uint64_t n_bit){$/;"	f
init_bloomfilter	bloom_filter.h	/^static inline BloomFilter* init_bloomfilter(size_t size, uint32_t n_seed){$/;"	f
init_cluster	cluster.c	/^Cluster* init_cluster(uint32_t max_mm, uint32_t exact_limit, uint32_t KMER_SIZE, uint32_t KMER_NUM){$/;"	f
init_ctgdb	mergecontig.c	/^CtgDB* init_ctgdb(void ) {$/;"	f
init_delimiters	file_reader.c	/^int* init_delimiters(char *expr){$/;"	f
init_div	divide.c	/^Div* init_div(uint32_t k_allele, uint32_t K_allele, float min_freq){$/;"	f
init_ef	asm_R2.c	/^EF* init_ef(uint32_t ef_id, char *eseq, uint32_t rd_len, uint32_t min_ol, float min_sm){$/;"	f
init_hashset_macro	hashset.h	63;"	d
init_heap	heap.h	/^static inline Heap* init_heap(heap_comp_func cmp, void *ref){$/;"	f
init_memvec	vector.h	/^static inline void init_memvec(Vector *vec, unsigned int e_size, unsigned int init_size){$/;"	f
init_merger	mergectg.c	/^merge_t* init_merger(uint32_t min_kmer, uint32_t min_overlap, float het, uint32_t kmersize, uint32_t max_cluster, uint32_t need_asm) {$/;"	f
init_simpasm	simp_asm.h	/^static inline SimpAssembler* init_simpasm(uint32_t n_cpu, uint32_t kmer_size, uint32_t rd_len, uint32_t strand, uint32_t min_ol, float min_sm, uint32_t max_mm, int allow_gap){$/;"	f
init_string	string.h	/^static inline String* init_string(int cap){$/;"	f
init_vec	vector.h	/^static inline Vector* init_vec(unsigned int e_size, unsigned int init_size){$/;"	f
is_entity_del	hashset.h	55;"	d
is_entity_null	hashset.h	54;"	d
is_fq	file_reader.h	/^	int is_fq;$/;"	m	struct:__anon32
is_similar_enough	mergectg.c	/^int is_similar_enough(merge_t *merger, contig_t *c1, contig_t *c2) {$/;"	f
iter_bitvec	bitvec.h	/^static inline uint64_t iter_bitvec(BitVec *bitv){$/;"	f
iter_hashset_macro	hashset.h	237;"	d
iter_idx	bitvec.h	/^	uint64_t iter_idx;$/;"	m	struct:__anon54
iter_idx	simp_asm.h	/^	uint32_t iter_idx;$/;"	m	struct:__anon51
iter_simpasm	simp_asm.h	/^static inline SimpContigInfo* iter_simpasm(SimpAssembler *sa){$/;"	f
j	stdaln.h	/^	int i, j;$/;"	m	struct:__anon15
jenkins_one_at_a_time_hash	hashset.h	/^static inline uint32_t jenkins_one_at_a_time_hash(char *key, size_t len){$/;"	f
k_allele	rainbow.h	/^	uint32_t k_allele, K_allele;$/;"	m	struct:__anon23
key	hashset.h	/^typedef struct { char *key; uint32_t val; } cuhash_t;$/;"	m	struct:__anon28
key	hashset.h	/^typedef struct { uint32_t key, val; } uuhash_t;$/;"	m	struct:__anon27
key	mergectg.h	/^typedef struct {uint32_t key; uint32_t oldid; char *path;} uuchash_t;$/;"	m	struct:__anon6
kmer	asm_R2.h	/^	uint32_t kmer:10, rps_idx:22;$/;"	m	struct:__anon36
kmer	mergecontig.h	/^	uint64_t kmer;$/;"	m	struct:__anon41
kmer	mergectg.h	/^	uint64_t kmer, kpos;$/;"	m	struct:__anon5
kmer	mergectg.h	/^	uint64_t kmer:62, kpos:2;$/;"	m	struct:__anon2
kmer1	rainbow.h	/^	uint32_t kmer1, kmer2, seqid;$/;"	m	struct:__anon17
kmer2	rainbow.h	/^	uint32_t kmer1, kmer2, seqid;$/;"	m	struct:__anon17
kmer_code	mergecontig.h	41;"	d
kmer_code	mergectg.h	72;"	d
kmer_eq	mergecontig.h	42;"	d
kmer_eq	mergectg.h	73;"	d
kmer_equals	rainbow.h	46;"	d
kmer_hashcode	rainbow.h	45;"	d
kmer_mask	dna.h	105;"	d
kmer_pos_t	mergecontig.h	/^} kmer_pos_t;$/;"	t	typeref:struct:__anon42
kmer_t	rainbow.h	/^} kmer_t;$/;"	t	typeref:struct:__anon17
kmer_tt	mergecontig.h	/^} kmer_tt;$/;"	t	typeref:struct:__anon41
kpos	mergecontig.h	/^	uint64_t kpos;$/;"	m	struct:__anon41
kpos	mergectg.h	/^	uint64_t kmer, kpos;$/;"	m	struct:__anon5
kpos	mergectg.h	/^	uint64_t kmer:62, kpos:2;$/;"	m	struct:__anon2
l	ezmsim.c	/^	int l, m; \/* length and maximum buffer size *\/$/;"	m	struct:__anon24	file:
l	ezmsim.c	/^	int l, m; \/* length and maximum buffer size *\/$/;"	m	struct:__anon25	file:
l	ezmsim.c	/^	uint64_t l, m;$/;"	m	struct:__anon26	file:
l_ol	asm_R2.h	/^	uint32_t l_rid:20, r_rid:20, l_ol:8, r_ol:8, n_mm:7, used:1;$/;"	m	struct:__anon39
l_rid	asm_R2.h	/^	uint32_t l_rid:20, r_rid:20, l_ol:8, r_ol:8, n_mm:7, used:1;$/;"	m	struct:__anon39
last	mergecontig.h	/^	uint64_t last; \/\/last kmer position$/;"	m	struct:__anon44
last	mergectg.h	/^	uint64_t last; \/\/last kmer position$/;"	m	struct:__anon7
last_brk	file_reader.h	/^	int last_brk;$/;"	m	struct:__anon31
lastoffset	mergecontig.h	/^	uint32_t lastoffset;$/;"	m	struct:__anon42
lastoffset	mergecontig.h	/^	uint32_t lastoffset;$/;"	m	struct:__anon43
left	mergectg.h	/^	pathtree_t *left;$/;"	m	struct:pathtree_t
len	aln_cigar.h	/^	uint16_t len:13, type:3;$/;"	m	struct:__anon56
len	asm_R2.h	/^	uint32_t len:31, closed:1;$/;"	m	struct:__anon38
len	mergetag.c	/^	uint32_t gid, off, len;$/;"	m	struct:__anon13	file:
len	rainbow.h	/^	uint32_t len;$/;"	m	struct:__anon19
len	simp_asm.h	/^	uint32_t len:31, closed:1;$/;"	m	struct:__anon50
len	simp_asm.h	/^	uint32_t seqid, len;$/;"	m	struct:__anon49
len1	mergetag.c	/^	uint32_t rid, cid, gid, rank, off1, len1, off2, len2;$/;"	m	struct:__anon12	file:
len2	mergetag.c	/^	uint32_t rid, cid, gid, rank, off1, len1, off2, len2;$/;"	m	struct:__anon12	file:
lend_ctgv_merger	mergectg.c	/^contig_t* lend_ctgv_merger(merge_t *merger) {$/;"	f
lend_ulist_div	divide.c	/^u32list* lend_ulist_div(Div *div){$/;"	f
line	file_reader.h	/^	String *line;$/;"	m	struct:__anon31
line_breaker	file_reader.h	/^	char line_breaker;$/;"	m	struct:__anon31
link_t	mergecontig.h	/^} link_t;$/;"	t	typeref:struct:__anon44
link_t	mergectg.h	/^} link_t;$/;"	t	typeref:struct:__anon7
linking_core	cluster.c	/^uint32_t linking_core(Cluster *cluster, uint32_t seqid, uint64_t *seq, uint32_t seqlen){$/;"	f
links	rainbow.h	/^	u32list *links;$/;"	m	struct:__anon20
load_ctgdb	mergecontig.c	/^CtgDB* load_ctgdb(FileReader *fr1, FileReader *fr2) {$/;"	f
load_hashset_macro	hashset.h	293;"	d
load_seqdb	cluster.c	/^SeqDB* load_seqdb(FileReader *fr, int is_fq, int fix_rd_len){$/;"	f
m	ezmsim.c	/^	int l, m; \/* length and maximum buffer size *\/$/;"	m	struct:__anon24	file:
m	ezmsim.c	/^	int l, m; \/* length and maximum buffer size *\/$/;"	m	struct:__anon25	file:
m	ezmsim.c	/^	uint64_t l, m;$/;"	m	struct:__anon26	file:
m_idx	mergectg.h	/^	idxv *m_idx;  \/\/ merged multiple index$/;"	m	struct:__anon3
m_rds	mergectg.h	/^	u32list *m_rds;  \/\/ merged reads index$/;"	m	struct:__anon3
main	ezmsim.c	/^int main (int argc, char *argv[])$/;"	f
main	main.c	/^int main(int argc, char **argv){$/;"	f
main	mergetag.c	/^int main(int argc, char **argv){$/;"	f
main	rbasm_main.c	/^int main(int argc, char **argv){$/;"	f
maq_mut_diref	ezmsim.c	/^void maq_mut_diref(const seq_t *seq, int is_hap, mutseq_t *hap1, mutseq_t *hap2)$/;"	f
maq_print_mutref	ezmsim.c	/^void maq_print_mutref(const char *name, const seq_t *seq, mutseq_t *hap1, mutseq_t *hap2)$/;"	f
markers	rainbow.h	/^	u64list *markers[4];$/;"	m	struct:__anon23
matrix	stdaln.h	/^	int *matrix;$/;"	m	struct:__anon14
max_cluster	mergectg.h	/^	uint32_t max_cluster; \/\/parameter$/;"	m	struct:__anon8
max_mm	rainbow.h	/^	uint32_t max_mm;$/;"	m	struct:__anon20
max_pair_len	rainbow.h	/^	uint32_t max_pair_len;$/;"	m	struct:__anon20
max_rd_len	rainbow.h	/^	uint8_t  rd_len, max_rd_len;$/;"	m	struct:__anon18
max_read	mergectg.h	/^	uint32_t max_read; \/\/ parameter for asm$/;"	m	struct:__anon8
max_seq_len	file_reader.h	/^	int max_seq_len;$/;"	m	struct:__anon32
max_seqid	rainbow.h	/^	uint32_t max_seqid;$/;"	m	struct:__anon20
merge_along_tree	mergectg.c	/^void merge_along_tree(merge_t *merger, pathtree_t *tree) {$/;"	f
merge_core	mergectg.c	/^void merge_core(merge_t *merger) {$/;"	f
merge_core	mergetag.c	/^void merge_core(recv *divs, String *seqs, uint32_t max_mm, int task, blockv *blocks, FILE *out){$/;"	f
merge_ctgs	mergectg.c	/^void merge_ctgs(merge_t *merger, FileReader *in, FILE *out) {$/;"	f
merge_invoker	main.c	/^int merge_invoker(int argc, char **argv) {$/;"	f
merge_leaves	mergectg.c	/^void merge_leaves(merge_t *merger, uint32_t id1, uint32_t id2) {$/;"	f
merge_t	mergectg.h	/^} merge_t;$/;"	t	typeref:struct:__anon8
min_freq	rainbow.h	/^	float min_freq;$/;"	m	struct:__anon23
min_kmer	mergectg.h	/^	uint32_t min_kmer; \/\/ parameter: # kmers to define two similar contigs$/;"	m	struct:__anon8
min_ol	asm_R2.h	/^	uint32_t min_ol;$/;"	m	struct:__anon40
min_ol	mergectg.h	/^	uint32_t min_ol; \/\/parameter for asm$/;"	m	struct:__anon8
min_overlap	mergectg.h	/^	uint32_t min_overlap; \/\/ parameter$/;"	m	struct:__anon8
min_read	mergectg.h	/^	uint32_t min_read; \/\/ parameter for asm$/;"	m	struct:__anon8
min_seq_len	file_reader.h	/^	int min_seq_len;$/;"	m	struct:__anon32
min_sm	asm_R2.h	/^	float    min_sm;$/;"	m	struct:__anon40
min_sm	mergectg.h	/^	float min_sm; \/\/ parameter for asm$/;"	m	struct:__anon8
mut_t	ezmsim.c	/^typedef unsigned short mut_t;$/;"	t	file:
mutmsk	ezmsim.c	/^static mut_t mutmsk = (mut_t)0xf000;$/;"	v	file:
mutseq_t	ezmsim.c	/^} mutseq_t;$/;"	t	typeref:struct:__anon25	file:
muttype_t	ezmsim.c	/^enum muttype_t {NOCHANGE = 0, INSERT = 0x1000, SUBSTITUTE = 0xe000, DELETE = 0xf000};$/;"	g	file:
n_bit	bitvec.h	/^	uint64_t n_bit;$/;"	m	struct:__anon54
n_cap	bitvec.h	/^	uint64_t n_cap;$/;"	m	struct:__anon54
n_col	rainbow.h	/^	uint32_t n_col;$/;"	m	struct:__anon23
n_mm	asm_R2.h	/^	uint32_t l_rid:20, r_rid:20, l_ol:8, r_ol:8, n_mm:7, used:1;$/;"	m	struct:__anon39
n_rd	rainbow.h	/^	uint32_t n_rd;$/;"	m	struct:__anon18
n_seed	bloom_filter.h	/^	uint32_t n_seed, seed_off;$/;"	m	struct:__anon34
name	file_reader.h	/^	String name;$/;"	m	struct:__anon29
native_number_cmp	list.h	216;"	d
need_asm	mergectg.h	/^	uint32_t need_asm; \/\/ parameter$/;"	m	struct:__anon8
nst_nt4_table	ezmsim.c	/^uint8_t nst_nt4_table[256] = {$/;"	v
num_cmp_script	sort.h	27;"	d
num_max	list.h	34;"	d
num_min	list.h	33;"	d
off	mergetag.c	/^	uint32_t gid, off, len;$/;"	m	struct:__anon13	file:
off1	mergetag.c	/^	uint32_t rid, cid, gid, rank, off1, len1, off2, len2;$/;"	m	struct:__anon12	file:
off2	mergetag.c	/^	uint32_t rid, cid, gid, rank, off1, len1, off2, len2;$/;"	m	struct:__anon12	file:
offset	mergecontig.h	/^	uint32_t offset;$/;"	m	struct:__anon42
offset	mergecontig.h	/^	uint32_t offset;$/;"	m	struct:__anon43
offset	mergecontig.h	/^	uint32_t offset;$/;"	m	struct:__anon44
offset	mergectg.h	/^	int offset;  \/\/ offset w.r.t. the current contig$/;"	m	struct:__anon5
offset	mergectg.h	/^	int offset; \/\/ current kmer offset$/;"	m	struct:__anon7
offset2	mergectg.h	/^	int offset2; \/\/ offset of query contig$/;"	m	struct:__anon5
olbisearch	mergecontig.c	/^static inline int olbisearch(uint64_t a[], uint64_t q, int i, int j) {$/;"	f	file:
old_clsid	mergecontig.h	/^	uint32_t old_clsid;$/;"	m	struct:__anon45
oldid	mergectg.h	/^typedef struct {uint32_t key; uint32_t oldid; char *path;} uuchash_t;$/;"	m	struct:__anon6
ols	asm_R2.h	/^	Vector   *ols;$/;"	m	struct:__anon40
ols	simp_asm.h	/^	sr_hitv  *ols;$/;"	m	struct:__anon51
one2bitvec	bitvec.h	/^static inline void one2bitvec(BitVec *bitv){ encap_bitvec(bitv, 1); one_bitvec(bitv, bitv->n_bit); bitv->n_bit ++; }$/;"	f
one_bitvec	bitvec.h	/^static inline void one_bitvec(BitVec *bitv, uint64_t idx){ bitv->bits[idx>>6] |= 1LLU << (idx&0x3FU); }$/;"	f
ones_bitvec	bitvec.h	/^static inline void ones_bitvec(BitVec *bitv){ memset(bitv->bits, 0xFFU, bitv->n_cap \/ 8); }$/;"	f
open_bif	file_reader.h	/^static inline BufferedInputFile* open_bif(char *filename){$/;"	f
open_bif2	file_reader.h	/^static inline BufferedInputFile* open_bif2(char *filename, char *suffix){$/;"	f
open_file_for_append	file_reader.h	/^static inline FILE* open_file_for_append(char *name, char *suffix){$/;"	f
open_file_for_read	file_reader.h	/^static inline FILE* open_file_for_read(char *name, char *suffix){$/;"	f
open_file_for_write	file_reader.h	/^static inline FILE* open_file_for_write(char *name, char *suffix){$/;"	f
out1	stdaln.h	/^	char *out1, *out2; \/* print them, and then you will know *\/$/;"	m	struct:__anon16
out2	stdaln.h	/^	char *out1, *out2; \/* print them, and then you will know *\/$/;"	m	struct:__anon16
outm	stdaln.h	/^	char *outm;$/;"	m	struct:__anon16
output_ef_ctgs	asm_R2.c	/^void output_ef_ctgs(EF *ef, FILE *out){$/;"	f
overlap	mergecontig.h	/^	uint32_t overlap;$/;"	m	struct:__anon47
path	mergectg.h	/^	String *path;$/;"	m	struct:__anon3
path	mergectg.h	/^typedef struct {uint32_t key; uint32_t oldid; char *path;} uuchash_t;$/;"	m	struct:__anon6
path	stdaln.h	/^	path_t *path; \/* for advanced users... :-) *\/$/;"	m	struct:__anon16
path_len	stdaln.h	/^	int path_len; \/* for advanced users... :-) *\/$/;"	m	struct:__anon16
path_t	stdaln.h	/^} path_t;$/;"	t	typeref:struct:__anon15
pathtree_t	mergectg.h	/^struct pathtree_t {$/;"	s
pathtree_t	mergectg.h	/^typedef struct pathtree_t pathtree_t;$/;"	t	typeref:struct:pathtree_t
peer_heap	heap.h	/^static inline void* peer_heap(Heap *heap){ return (count_rjheapv(heap->ptrs)? get_rjheapv(heap->ptrs, 0) : NULL );}$/;"	f
poisson_num_gen	ezmsim.c	/^int poisson_num_gen(double lamda)$/;"	f
pool_ctg	asm_R2.h	/^	Vector   *pool_ctg;$/;"	m	struct:__anon40
pool_vec	asm_R2.h	/^	Vector   *pool_vec;$/;"	m	struct:__anon40
pop_heap	heap.h	/^static inline void* pop_heap(Heap *heap){$/;"	f
pop_vec	vector.h	/^static inline int pop_vec(Vector *vec, void *e){$/;"	f
pos	mergecontig.h	/^	uint64_t pos;$/;"	m	struct:__anon42
prefix_path	mergectg.c	/^void prefix_path(char *s1, char *s2, int n, char *pre) {$/;"	f
prepare_hashset_macro	hashset.h	117;"	d
prepare_reads	mergectg.c	/^void prepare_reads(merge_t *merger, FileReader *in, uint32_t lastcid) {$/;"	f
prepare_seq_seqdb	cluster.c	/^uint8_t prepare_seq_seqdb(SeqDB *sdb, uint32_t rid, uint64_t *seqs){$/;"	f
print_alignments	asm_R2.c	/^void print_alignments(EF *ef){$/;"	f
print_asm	mergectg.c	/^void print_asm(merge_t *merger, FILE *out) {$/;"	f
print_asm2	mergectg.c	/^void print_asm2(merge_t *merger, FILE *out) {$/;"	f
print_clusters	mergecontig.c	/^void print_clusters(PWDB *db) {$/;"	f
print_ctgdb	mergecontig.c	/^void print_ctgdb(CtgDB *db) {$/;"	f
print_pretty_seq	file_reader.h	/^static inline void print_pretty_seq(FILE *out, String *seq, int line_width){$/;"	f
ps1	rainbow.h	/^	u32list *ps1;$/;"	m	struct:__anon23
ps2	rainbow.h	/^	u32list *ps2;$/;"	m	struct:__anon23
ptr	file_reader.h	/^	int ptr;$/;"	m	struct:__anon31
ptrs	heap.h	/^	rjheapv *ptrs;$/;"	m	struct:__anon11
push_heap	heap.h	/^static inline void push_heap(Heap *heap, void *p){$/;"	f
push_simpasm	simp_asm.h	/^static inline void push_simpasm(SimpAssembler *sa, uint32_t seqid, char *seq, uint32_t seqlen, uint8_t rank){$/;"	f
push_vec	vector.h	/^static inline void push_vec(Vector *vec, void *e){$/;"	f
put_bloomfilter	bloom_filter.h	/^static inline void put_bloomfilter(BloomFilter *bf, const void *key, uint32_t len){$/;"	f
put_cache_ctgs	mergectg.c	/^void put_cache_ctgs(merge_t *merger, contig_t *ctg) {$/;"	f
put_hashset_macro	hashset.h	205;"	d
put_pool_ctg	asm_R2.c	/^void put_pool_ctg(EF *ef, FContig *ctg){$/;"	f
put_pool_vec	asm_R2.c	/^void put_pool_vec(EF *ef, Vector *vec){$/;"	f
pw_aln_contigs	mergecontig.c	/^PWDB* pw_aln_contigs(CtgDB *db, uint32_t min_overlap, float het) {$/;"	f
pw_aln_contigs_brute	mergecontig.c	/^PWDB* pw_aln_contigs_brute(CtgDB *db) {$/;"	f
pwctgs	mergecontig.h	/^	pwctglist *pwctgs;$/;"	m	struct:__anon48
qsort_vec	vector.h	/^static inline void qsort_vec(Vector *vec, cmp_vec_fun fun){$/;"	f
qual	file_reader.h	/^	String qual;$/;"	m	struct:__anon29
r2r	simp_asm.h	/^	u64hash  *r2r;$/;"	m	struct:__anon51
r_ol	asm_R2.h	/^	uint32_t l_rid:20, r_rid:20, l_ol:8, r_ol:8, n_mm:7, used:1;$/;"	m	struct:__anon39
r_rid	asm_R2.h	/^	uint32_t l_rid:20, r_rid:20, l_ol:8, r_ol:8, n_mm:7, used:1;$/;"	m	struct:__anon39
ran_normal	ezmsim.c	/^double ran_normal()$/;"	f
rank	asm_R2.h	/^	uint32_t rd_len:10, rank:10;$/;"	m	struct:__anon37
rank	mergectg.h	/^	uint32_t rank;$/;"	m	struct:__anon1
rank	mergetag.c	/^	uint32_t rid, cid, gid, rank, off1, len1, off2, len2;$/;"	m	struct:__anon12	file:
rank	rainbow.h	/^	uint32_t seqid, seqoff, seqlen1:10, seqlen2:10, rank:6, revsed:6;$/;"	m	struct:__anon21
rank	simp_asm.h	/^	uint32_t ctg_id, ctg_dir:1, ctg_off:20, used:1, rank:10;$/;"	m	struct:__anon49
rank_bitvec	bitvec.h	/^static inline uint64_t rank_bitvec(BitVec *bitv, uint64_t idx){$/;"	f
rank_cigars_seqlen	aln_cigar.h	/^static inline int rank_cigars_seqlen(AlnCigar *cigars, int n_cigar, int len, int seq_idx){$/;"	f
rd_kmer_code	mergectg.h	26;"	d
rd_kmer_eq	mergectg.h	27;"	d
rd_kmer_t	mergectg.h	/^} rd_kmer_t;$/;"	t	typeref:struct:__anon2
rd_len	asm_R2.h	/^	uint32_t rd_len:10, rank:10;$/;"	m	struct:__anon37
rd_len	mergectg.h	/^	uint32_t rd_len;$/;"	m	struct:__anon1
rd_len	rainbow.h	/^	uint8_t  rd_len, max_rd_len;$/;"	m	struct:__anon18
rds	asm_R2.h	/^	Vector   *rds;$/;"	m	struct:__anon40
rds	mergectg.h	/^	readv *rds;$/;"	m	struct:__anon3
rds	rainbow.h	/^	rilist *rds;$/;"	m	struct:__anon23
rds	simp_asm.h	/^	seqv     *rds;$/;"	m	struct:__anon51
read_bif	file_reader.h	/^static inline int64_t read_bif(BufferedInputFile *bif, void *data, int64_t size){$/;"	f
read_t	mergectg.h	/^} read_t;$/;"	t	typeref:struct:__anon1
reduce_vec_size	vector.h	/^static inline int reduce_vec_size(Vector *vec, size_t size){$/;"	f
ref	heap.h	/^	void *ref;$/;"	m	struct:__anon11
ref_apply_array	sort.h	103;"	d
ref_iter_hashset_macro	hashset.h	251;"	d
refine_cigars	aln_cigar.h	/^static inline int refine_cigars(AlnCigar *c, int n){$/;"	f
remove_hashset_macro	hashset.h	211;"	d
remove_heap	heap.h	/^static inline void remove_heap(Heap *heap, size_t idx){$/;"	f
reset_div	divide.c	/^void reset_div(Div *div){$/;"	f
reset_ef	asm_R2.c	/^void reset_ef(EF *ef, uint32_t ef_id, char *eseq, uint32_t rd_len, uint32_t min_ol, float min_sm){$/;"	f
reset_filereader	file_reader.c	/^int reset_filereader(FileReader *fr){$/;"	f
reset_iter_hashset_macro	hashset.h	235;"	d
reset_merger	mergectg.c	/^void reset_merger(merge_t *merger) {$/;"	f
reset_simpasm	simp_asm.h	/^static inline void reset_simpasm(SimpAssembler *sa){$/;"	f
reset_vec	vector.h	/^static inline void reset_vec(Vector *vec){$/;"	f
return_ctgv_merger	mergectg.c	/^void return_ctgv_merger(merge_t *merger, contig_t *ctg) {$/;"	f
return_ulist_div	divide.c	/^void return_ulist_div(Div *div, u32list *list){ if(list){ clear_u32list(list); push_u32slist(div->cache, list); } }$/;"	f
rev_rank_cigars_seqlen	aln_cigar.h	/^static inline int rev_rank_cigars_seqlen(AlnCigar *cigars, int n_cigar, int len, int seq_idx){$/;"	f
rev_select_cigars_seqlen	aln_cigar.h	/^static inline int rev_select_cigars_seqlen(AlnCigar *cigars, int n_cigar, int len, int seq_idx){$/;"	f
reverse_cigars	aln_cigar.h	/^static inline void reverse_cigars(AlnCigar *cs, int n){$/;"	f
reverse_dna	dna.h	/^static inline void reverse_dna(char *seq, int len){$/;"	f
reverse_string	string.h	/^static inline void reverse_string(String *str){$/;"	f
reverse_vec	vector.h	/^static inline void reverse_vec(Vector *vec){$/;"	f
revsed	rainbow.h	/^	uint32_t seqid, seqoff, seqlen1:10, seqlen2:10, rank:6, revsed:6;$/;"	m	struct:__anon21
revseq2bits	dna.h	/^static inline void revseq2bits(uint64_t *bits, uint64_t bitoff, char *seq, uint32_t seqlen){$/;"	f
rhash_code	asm_R2.h	40;"	d
rhash_eq	asm_R2.h	41;"	d
rhash_t	asm_R2.h	/^} rhash_t;$/;"	t	typeref:struct:__anon36
rid	asm_R2.h	/^typedef struct { uint32_t rid:16, roff:16; } rp_t;$/;"	m	struct:__anon35
rid	mergetag.c	/^	uint32_t rid, cid, gid, rank, off1, len1, off2, len2;$/;"	m	struct:__anon12	file:
rids	asm_R2.h	/^	Vector   *rids;$/;"	m	struct:__anon38
rids	simp_asm.h	/^	u32list  *rids;$/;"	m	struct:__anon51
right	mergectg.h	/^	pathtree_t *right;$/;"	m	struct:pathtree_t
roff	asm_R2.h	/^typedef struct { uint32_t rid:16, roff:16; } rp_t;$/;"	m	struct:__anon35
row	stdaln.h	/^	int row;$/;"	m	struct:__anon14
rp_t	asm_R2.h	/^typedef struct { uint32_t rid:16, roff:16; } rp_t;$/;"	t	typeref:struct:__anon35
rps	asm_R2.h	/^	Vector   *rps;$/;"	m	struct:__anon40
rps_idx	asm_R2.h	/^	uint32_t kmer:10, rps_idx:22;$/;"	m	struct:__anon36
s	ezmsim.c	/^	mut_t *s; \/* sequence *\/$/;"	m	struct:__anon25	file:
s	ezmsim.c	/^	unsigned char *s; \/* sequence *\/$/;"	m	struct:__anon24	file:
sbts	rainbow.h	/^	sbtv    *sbts;$/;"	m	struct:__anon20
score	mergecontig.h	/^	int score; $/;"	m	struct:__anon47
score	stdaln.h	/^	int score; \/* score *\/$/;"	m	struct:__anon16
sdb	rainbow.h	/^	SeqDB    *sdb, *sdb2;$/;"	m	struct:__anon20
sdb2	rainbow.h	/^	SeqDB    *sdb, *sdb2;$/;"	m	struct:__anon20
search_array	vector.h	159;"	d
search_array_dsc	vector.h	168;"	d
seed_off	bloom_filter.h	/^	uint32_t n_seed, seed_off;$/;"	m	struct:__anon34
seeds	bloom_filter.h	/^static const uint32_t seeds[20] = $/;"	v
select_cigars_seqlen	aln_cigar.h	/^static inline int select_cigars_seqlen(AlnCigar *cigars, int n_cigar, int len, int seq_idx){$/;"	f
seq	asm_R2.h	/^	String   *seq;$/;"	m	struct:__anon38
seq	asm_R2.h	/^	char     seq[MAX_RD_LEN+1];$/;"	m	struct:__anon37
seq	file_reader.h	/^	String seq;$/;"	m	struct:__anon29
seq	mergecontig.h	/^	char *seq;$/;"	m	struct:__anon45
seq	mergectg.h	/^	char *seq;$/;"	m	struct:__anon4
seq	mergectg.h	/^	char seq[MAX_RD_LEN+1];$/;"	m	struct:__anon1
seq	rainbow.h	/^	uint64_t seq[8];$/;"	m	struct:__anon19
seq	simp_asm.h	/^	String   *seq;$/;"	m	struct:__anon50
seq1	rainbow.h	/^	uint64_t seq1[10], seq2[10];$/;"	m	struct:__anon20
seq2	rainbow.h	/^	uint64_t seq1[10], seq2[10];$/;"	m	struct:__anon20
seq2bits	dna.h	/^static inline void seq2bits(uint64_t *bits, uint64_t bitoff, char *seq, uint32_t seqlen){$/;"	f
seq2kmer	dna.h	/^static inline uint64_t seq2kmer(char *seq, uint32_t ksize){$/;"	f
seq2revkmer	dna.h	/^static inline uint64_t seq2revkmer(char *seq, uint32_t ksize){$/;"	f
seq_id	asm_R2.h	/^	uint32_t seq_id;$/;"	m	struct:__anon37
seq_id	mergectg.h	/^	uint32_t seq_id;$/;"	m	struct:__anon1
seq_read_fasta	ezmsim.c	/^int seq_read_fasta(FILE *fp, seq_t *seq, char *locus, char *comment)$/;"	f
seq_set_block_size	ezmsim.c	/^void seq_set_block_size(int size)$/;"	f
seq_t	ezmsim.c	/^} seq_t;$/;"	t	typeref:struct:__anon24	file:
seqid	rainbow.h	/^	uint32_t kmer1, kmer2, seqid;$/;"	m	struct:__anon17
seqid	rainbow.h	/^	uint32_t seqid, seqoff, seqlen1:10, seqlen2:10, rank:6, revsed:6;$/;"	m	struct:__anon21
seqid	simp_asm.h	/^	uint32_t seqid, len;$/;"	m	struct:__anon49
seqlen1	rainbow.h	/^	uint32_t seqid, seqoff, seqlen1:10, seqlen2:10, rank:6, revsed:6;$/;"	m	struct:__anon21
seqlen2	rainbow.h	/^	uint32_t seqid, seqoff, seqlen1:10, seqlen2:10, rank:6, revsed:6;$/;"	m	struct:__anon21
seqlens	rainbow.h	/^	u8list  *seqlens;$/;"	m	struct:__anon18
seqoff	rainbow.h	/^	uint32_t seqid, seqoff, seqlen1:10, seqlen2:10, rank:6, revsed:6;$/;"	m	struct:__anon21
seqoffs	rainbow.h	/^	u64list *seqoffs;$/;"	m	struct:__anon18
seqs	rainbow.h	/^	u8list *seqs;$/;"	m	struct:__anon23
seqs	rainbow.h	/^	uint64_t *seqs;$/;"	m	struct:__anon18
set_D	stdaln.c	278;"	d	file:
set_I	stdaln.c	256;"	d	file:
set_M	stdaln.c	240;"	d	file:
set_end_D	stdaln.c	288;"	d	file:
set_end_I	stdaln.c	266;"	d	file:
set_entity_del	hashset.h	58;"	d
set_entity_null	hashset.h	57;"	d
set_inc_tag_ef	asm_R2.c	/^void set_inc_tag_ef(EF *ef, uint32_t inc){$/;"	f
set_vec	vector.h	/^static inline void set_vec(Vector *vec, size_t idx, void *e){$/;"	f
set_vec_size	vector.h	/^static inline int set_vec_size(Vector *vec, size_t size){$/;"	f
sids	simp_asm.h	/^	u32list  *sids;$/;"	m	struct:__anon50
sim_pairs	mergectg.h	/^	uint32_t sim_pairs;$/;"	m	struct:__anon8
simple_assemble	simp_asm.h	/^static inline void simple_assemble(SimpAssembler *sa){$/;"	f
simple_join_contigs	simp_asm.h	/^static inline int simple_join_contigs(SimpAssembler *sa, SR_AlnHit *hit){$/;"	f
simple_move_rids	simp_asm.h	/^static inline void simple_move_rids(SimpAssembler *sa, uint32_t dst, uint32_t src, int off){$/;"	f
simple_reverse_contig	simp_asm.h	/^static inline void simple_reverse_contig(SimpAssembler *sa, uint32_t ctg_id){$/;"	f
size	bloom_filter.h	/^	size_t size;$/;"	m	struct:__anon34
size	file_reader.h	/^	int size;$/;"	m	struct:__anon31
size	string.h	/^	int  size;$/;"	m	struct:__anon53
size	string.h	/^	int size;$/;"	m	struct:__anon52
size	vector.h	/^	size_t size;$/;"	m	struct:Vector
sort_array	sort.h	48;"	d
sorting_core	cluster.c	/^uint32_t sorting_core(Cluster *cluster){$/;"	f
split_string	string.h	/^static inline int split_string(String *str, char separator, Vector *virtual_strings){$/;"	f
split_vstring	string.h	/^static inline int split_vstring(VirtualString *str, char separator, Vector *virtual_strings, int cut){$/;"	f
sra	simp_asm.h	/^	SR_SeqDB *sra;$/;"	m	struct:__anon51
start1	stdaln.h	/^	int start1, end1; \/* start and end of the first sequence, coordinations are 1-based *\/$/;"	m	struct:__anon16
start2	stdaln.h	/^	int start2, end2; \/* start and end of the second sequence, coordinations are 1-based *\/$/;"	m	struct:__anon16
stdin_filereader	file_reader.c	/^FileReader* stdin_filereader(){$/;"	f
strindex	ezmsim.c	/^int strindex(idx_t *index, unsigned char *s, unsigned char *t)$/;"	f
string	string.h	/^	char *string;$/;"	m	struct:__anon52
string	string.h	/^	char *string;$/;"	m	struct:__anon53
string2cigars	aln_cigar.h	/^static inline int string2cigars(AlnCigar *cigars, char *str, int len){$/;"	f
string_filereader	file_reader.c	/^FileReader* string_filereader(char *string){$/;"	f
sub32seqbits	dna.h	/^static inline uint64_t sub32seqbits(uint64_t *src, uint64_t off){$/;"	f
sub_cigars	aln_cigar.h	/^static inline int sub_cigars(AlnCigar *dst, AlnCigar *cigars, int n_cigar, int off, int len){$/;"	f
sub_seq_cigars	aln_cigar.h	/^static inline int sub_seq_cigars(AlnCigar *dst, AlnCigar *c, int n, int seq_idx, int off, int len){$/;"	f
substr	string.h	/^static inline char* substr(char *string, int start, int end, char *dst){$/;"	f
sums	bitvec.h	/^	uint64_t *sums;$/;"	m	struct:__anon54
swap_tmp	string.h	35;"	d
sys_prime_list	hashset.h	/^static const uint64_t sys_prime_list[61] = {$/;"	v
sz	mergecontig.h	/^	uint32_t sz;   \/\/union tree depth$/;"	m	struct:__anon45
tabs	file_reader.h	/^	Vector *tabs;$/;"	m	struct:__anon31
tid	mergectg.h	/^	uint32_t tid; \/\/ leaf records contig ID$/;"	m	struct:pathtree_t
tracing_core	cluster.c	/^void tracing_core(Cluster *cluster, uint32_t bt){$/;"	f
tree	mergectg.h	/^	pathtree_t *tree;$/;"	m	struct:__anon8
trim_string	string.h	/^static inline void trim_string(String *str){$/;"	f
trunc_string	string.h	/^static inline void trunc_string(String *str, int size){$/;"	f
type	aln_cigar.h	/^	uint16_t len:13, type:3;$/;"	m	struct:__anon56
u32hash_code	hashset.h	489;"	d
u32hashcode	hashset.h	480;"	d
u64hash_code	hashset.h	490;"	d
u64hashcode	hashset.h	481;"	d
uc	ezmsim.c	/^void uc(unsigned char *s)$/;"	f
uniq	asm_R2.h	/^	u64hash  *uniq;$/;"	m	struct:__anon40
update_ctg2merge	mergectg.c	/^void update_ctg2merge(merge_t *merger) {$/;"	f
usage	ezmsim.c	/^int usage()$/;"	f
usage	main.c	/^int usage(){$/;"	f
usage	mergetag.c	/^int usage(){$/;"	f
used	asm_R2.h	/^	uint32_t ctg_id:24, ctg_off:19, used:1;$/;"	m	struct:__anon37
used	asm_R2.h	/^	uint32_t l_rid:20, r_rid:20, l_ol:8, r_ol:8, n_mm:7, used:1;$/;"	m	struct:__anon39
used	simp_asm.h	/^	uint32_t ctg_id, ctg_dir:1, ctg_off:20, used:1, rank:10;$/;"	m	struct:__anon49
uuchash_code	mergectg.h	77;"	d
uuchash_equals	mergectg.h	78;"	d
uuchash_t	mergectg.h	/^typedef struct {uint32_t key; uint32_t oldid; char *path;} uuchash_t;$/;"	t	typeref:struct:__anon6
uuhash_code	hashset.h	504;"	d
uuhash_equals	hashset.h	505;"	d
uuhash_t	hashset.h	/^typedef struct { uint32_t key, val; } uuhash_t;$/;"	t	typeref:struct:__anon27
uxxhash_equals	hashset.h	491;"	d
val	hashset.h	/^typedef struct { char *key; uint32_t val; } cuhash_t;$/;"	m	struct:__anon28
val	hashset.h	/^typedef struct { uint32_t key, val; } uuhash_t;$/;"	m	struct:__anon27
vec_memcpy	vector.h	/^static inline void vec_memcpy(void *dst, void *src, size_t size){$/;"	f
vec_size	vector.h	65;"	d
version	main.c	/^const char *version = "2.0.1";$/;"	v
vline	file_reader.h	/^	String *vline;$/;"	m	struct:__anon31
xopen	ezmsim.c	103;"	d	file:
zero2bitvec	bitvec.h	/^static inline void zero2bitvec(BitVec *bitv){ encap_bitvec(bitv, 1); zero_bitvec(bitv, bitv->n_bit); bitv->n_bit ++; }$/;"	f
zero_bitvec	bitvec.h	/^static inline void zero_bitvec(BitVec *bitv, uint64_t idx){ bitv->bits[idx>>6] &= ~(1LLU << (idx&0x3FU)); }$/;"	f
zeros_bitvec	bitvec.h	/^static inline void zeros_bitvec(BitVec *bitv){ memset(bitv->bits, 0, bitv->n_cap \/ 8); }$/;"	f
