SYMBOL INDEX (264 symbols across 6 files) FILE: BAFregress.c function sqr (line 44) | KSORT_INIT_GENERIC(float) function run (line 102) | int run(int argc, char **argv) { FILE: affy2vcf.c function read_long (line 116) | static inline uint32_t read_long(hFILE *hfile) { function read_float (line 124) | static inline float read_float(hFILE *hfile) { function read_string8 (line 135) | static inline int32_t read_string8(hFILE *hfile, char **buffer) { function read_string16 (line 148) | static inline int32_t read_string16(hFILE *hfile, wchar_t **buffer) { type Cell (line 171) | typedef struct { type Entry (line 177) | typedef struct { type SubGrid (line 182) | typedef struct { type xda_cel_t (line 199) | typedef struct { function xda_cel_t (line 222) | static xda_cel_t *xda_cel_init(const char *fn, hFILE *hfile, int flags) { function xda_cel_destroy (line 280) | static void xda_cel_destroy(xda_cel_t *xda_cel) { function xda_cel_print (line 294) | static void xda_cel_print(const xda_cel_t *xda_cel, FILE *stream, int ve... type Parameter (line 346) | typedef struct { type DataHeader (line 354) | typedef struct DataHeader DataHeader; type DataHeader (line 356) | struct DataHeader { type ColHeader (line 367) | typedef struct { type DataSet (line 373) | typedef struct { type DataGroup (line 388) | typedef struct { type ColumnHeader (line 396) | typedef struct { type agcc_t (line 402) | typedef struct { function agcc_read_parameters (line 415) | static void agcc_read_parameters(Parameter *parameter, hFILE *hfile, int... function agcc_read_data_header (line 452) | static void agcc_read_data_header(DataHeader *data_header, hFILE *hfile,... function agcc_read_data_set (line 468) | static void agcc_read_data_set(DataSet *data_set, hFILE *hfile, int flag... function agcc_read_data_group (line 501) | static void agcc_read_data_group(DataGroup *data_group, hFILE *hfile, in... function agcc_t (line 516) | static agcc_t *agcc_init(const char *fn, hFILE *hfile, int flags) { function agcc_destroy_parameters (line 558) | static void agcc_destroy_parameters(Parameter *parameters, int32_t n_par... function agcc_destroy_data_header (line 568) | static void agcc_destroy_data_header(DataHeader *data_header) { function agcc_destroy_data_set (line 579) | static void agcc_destroy_data_set(DataSet *data_set) { function agcc_destroy_data_group (line 589) | static void agcc_destroy_data_group(DataGroup *data_group) { function agcc_destroy (line 596) | static void agcc_destroy(agcc_t *agcc) { function buffer_string16 (line 608) | static void buffer_string16(const uint16_t *value, int32_t n_value, size... function agcc_print_parameters (line 615) | static void agcc_print_parameters(const Parameter *parameters, int32_t n... function agcc_print_data_header (line 662) | static void agcc_print_data_header(const DataHeader *data_header, FILE *... function agcc_print_probe_set_name (line 673) | void agcc_print_probe_set_name(const char *s, FILE *stream) { function agcc_print_call (line 678) | void agcc_print_call(const char *s, FILE *stream) { function agcc_print_float (line 686) | void agcc_print_float(const char *s, FILE *stream) { function agcc_print_data_set (line 695) | static void agcc_print_data_set(const DataSet *data_set, FILE *stream, i... function agcc_print_data_group (line 753) | static void agcc_print_data_group(const DataGroup *data_group, FILE *str... function agcc_print (line 759) | static void agcc_print(const agcc_t *agcc, FILE *stream, int verbose) { function chps_to_tsv (line 769) | static void chps_to_tsv(uint8_t *magic, agcc_t **agcc, int n, FILE *stre... function parse_dat_header (line 856) | static void parse_dat_header(char *dat_header, char *str[12], int n_str[... function cels_to_tsv (line 937) | static void cels_to_tsv(uint8_t *magic, void **files, int n, FILE *strea... function htsFile (line 1060) | static htsFile *unheader(const char *fn, kstring_t *str) { type cluster_t (line 1101) | typedef struct { type snp_t (line 1111) | typedef struct { type snp_models_t (line 1119) | typedef struct { function brlmmp_cluster_init (line 1127) | static inline void brlmmp_cluster_init(const char *s, const int *off, cl... function birdseed_cluster_init (line 1137) | static inline void birdseed_cluster_init(const char *s, const int *off, ... function snp_models_t (line 1147) | static snp_models_t *snp_models_init(const char *fn) { function snp_models_destroy (line 1249) | static void snp_models_destroy(snp_models_t *snp_models) { type record_t (line 1263) | typedef struct { type annot_t (line 1273) | typedef struct { function annot_t (line 1286) | static annot_t *annot_init(const char *fn, const char *sam_fn, const cha... function annot_destroy (line 1509) | static void annot_destroy(annot_t *annot) { type varitr_t (line 1528) | typedef struct { function varitr_init_common (line 1549) | static void varitr_init_common(varitr_t *varitr) { function varitr_t (line 1560) | static varitr_t *varitr_init_cc(bcf_hdr_t *hdr, agcc_t **agcc, int n) { function varitr_t (line 1601) | static varitr_t *varitr_init_txt(bcf_hdr_t *hdr, const char *calls_fn, c... function check_probe_set_id (line 1661) | static inline void check_probe_set_id(char *dest, const char *src) { function varitr_loop (line 1670) | static int varitr_loop(varitr_t *varitr, void *probeset_ids) { function varitr_destroy (line 1819) | static void varitr_destroy(varitr_t *varitr) { function bcf_hdr_t (line 1841) | static bcf_hdr_t *hdr_init(const faidx_t *fai, int flags) { function adjust_clusters (line 2017) | static void adjust_clusters(const int *gts, const float *x, const float ... function update_info_cluster (line 2059) | static void update_info_cluster(const bcf_hdr_t *hdr, bcf1_t *rec, const... function compute_baf_lrr (line 2086) | static void compute_baf_lrr(const float *norm_x, const float *norm_y, in... function process (line 2120) | static void process(faidx_t *fai, const annot_t *annot, void *probeset_i... function parse_tags (line 2400) | static int parse_tags(const char *str) { function list_tags (line 2428) | static void list_tags(void) { function run (line 2440) | int run(int argc, char *argv[]) { FILE: gtc2vcf.c function read_array (line 74) | static void read_array(hFILE *hfile, void **arr, size_t *m_arr, size_t n... function read_pfx_array (line 96) | static void read_pfx_array(hFILE *hfile, void **arr, size_t *m_arr, size... function read_pfx_string (line 106) | static void read_pfx_string(hFILE *hfile, char **str, size_t *m_str) { function is_gzip (line 124) | static int is_gzip(hFILE *hfile) { type buffer_array_t (line 134) | typedef struct { function buffer_array_t (line 144) | static buffer_array_t *buffer_array_init(hFILE *hfile, size_t capacity, ... function get_element (line 158) | static int get_element(buffer_array_t *arr, void *dst, size_t item_idx) { function buffer_array_destroy (line 177) | static void buffer_array_destroy(buffer_array_t *arr) { type LocusEntry (line 190) | typedef struct { function get_assay_type (line 235) | static uint8_t get_assay_type(const char *allele_a_probe_seq, const char... function locusentry_read (line 267) | static void locusentry_read(LocusEntry *locus_entry, hFILE *hfile) { type bpm_t (line 330) | typedef struct { function bpm_t (line 365) | static bpm_t *bpm_init(const char *fn, int eof_check, int make_dict) { function bpm_destroy (line 436) | static void bpm_destroy(bpm_t *bpm) { function bpm_to_csv (line 479) | static void bpm_to_csv(const bpm_t *bpm, FILE *stream, int flags) { function tsv_read_uint8 (line 548) | static int tsv_read_uint8(tsv_t *tsv, bcf1_t *rec, void *usr) { function tsv_read_int32 (line 558) | static int tsv_read_int32(tsv_t *tsv, bcf1_t *rec, void *usr) { function tsv_read_float (line 568) | static int tsv_read_float(tsv_t *tsv, bcf1_t *rec, void *usr) { function tsv_read_string (line 578) | static int tsv_read_string(tsv_t *tsv, bcf1_t *rec, void *usr) { function csv_parse (line 592) | static int csv_parse(tsv_t *tsv, bcf1_t *rec, char *str) { function locus_merge (line 610) | static void locus_merge(LocusEntry *dest, LocusEntry *src) { function bpm_t (line 703) | static bpm_t *bpm_csv_init(const char *fn, bpm_t *bpm, int make_dict) { type ClusterStats (line 854) | typedef struct { type ClusterScore (line 862) | typedef struct { type ClusterRecord (line 869) | typedef struct { type egt_t (line 879) | typedef struct { function clusterscore_read (line 898) | static void clusterscore_read(ClusterScore *clusterscore, hFILE *hfile) { function clusterrecord_read (line 905) | static void clusterrecord_read(ClusterRecord *clusterrecord, hFILE *hfil... function egt_t (line 929) | static egt_t *egt_init(const char *fn, int eof_check) { function egt_destroy (line 1003) | static void egt_destroy(egt_t *egt) { function egt_to_csv (line 1022) | static void egt_to_csv(const egt_t *egt, FILE *stream, int verbose) { type chip_type_t (line 1094) | typedef struct { type RunInfo (line 1191) | typedef struct { type idat_t (line 1199) | typedef struct { function idat_read (line 1236) | static int idat_read(idat_t *idat, uint16_t id) { function idat_t (line 1334) | static idat_t *idat_init(const char *fn, int load_arrays) { function idat_destroy (line 1388) | static void idat_destroy(idat_t *idat) { function idat_to_csv (line 1422) | static void idat_to_csv(const idat_t *idat, FILE *stream, int verbose) { function idats_to_tsv (line 1464) | static void idats_to_tsv(idat_t **idats, int n, FILE *stream) { type XForm (line 1536) | typedef struct { type ScannerData (line 1554) | typedef struct { type SampleData (line 1562) | typedef struct { type gtc_t (line 1571) | typedef struct { function gtc_read (line 1620) | static int gtc_read(gtc_t *gtc, uint16_t id) { function gtc_t (line 1735) | static gtc_t *gtc_init(const char *fn, size_t capacity) { function gtc_destroy (line 1773) | static void gtc_destroy(gtc_t *gtc) { function gtc_to_csv (line 1809) | static void gtc_to_csv(const gtc_t *gtc, FILE *stream, int verbose) { function gtcs_to_tsv (line 1901) | static void gtcs_to_tsv(gtc_t **gtcs, int n, FILE *stream) { function bpm_t (line 1940) | static bpm_t *sam_csv_init(const char *fn, bpm_t *bpm, const char *genom... function raw_x_y2norm_x_y (line 1990) | static inline void raw_x_y2norm_x_y(uint16_t raw_x, uint16_t raw_y, floa... function norm_x_y2ilmn_theta_r (line 2003) | static inline void norm_x_y2ilmn_theta_r(float norm_x, float norm_y, flo... function adjust_clusters (line 2008) | static void adjust_clusters(const uint8_t *gts, const float *ilmn_theta,... function rev_allele (line 2055) | static inline char rev_allele(char allele) { function gtcs_to_gs (line 2065) | static void gtcs_to_gs(gtc_t **gtc, int n, const bpm_t *bpm, const egt_t... function bcf_hdr_t (line 2186) | static bcf_hdr_t *hdr_init(const faidx_t *fai, int flags) { function gts_to_gt_arr (line 2325) | static int gts_to_gt_arr(int32_t *gt_arr, const uint8_t *gts, int n, int... function locus2bcf (line 2352) | static int locus2bcf(const LocusEntry *locus_entry, const ClusterRecord ... function gtcs_to_vcf (line 2485) | static void gtcs_to_vcf(faidx_t *fai, const bpm_t *bpm, const egt_t *egt... type gs_col_t (line 2629) | typedef struct { function tsv_setter_gs_col (line 2635) | static int tsv_setter_gs_col(tsv_t *tsv, bcf1_t *rec, void *usr) { function tsv_setter_chrom_flexible (line 2680) | static int tsv_setter_chrom_flexible(tsv_t *tsv, bcf1_t *rec, void *usr) { function tsv_setter_ilmn_strand (line 2688) | static int tsv_setter_ilmn_strand(tsv_t *tsv, bcf1_t *rec, void *usr) { function tsv_setter_snp (line 2694) | static int tsv_setter_snp(tsv_t *tsv, bcf1_t *rec, void *usr) { function tsv_register_all (line 2703) | static int tsv_register_all(tsv_t *tsv, const char *id, tsv_setter_t set... function tsv_parse_delimiter (line 2715) | static int tsv_parse_delimiter(tsv_t *tsv, bcf1_t *rec, char *str, int d... function gs_to_vcf (line 2739) | static void gs_to_vcf(faidx_t *fai, const bpm_t *bpm, const egt_t *egt, ... function parse_tags (line 3242) | static int parse_tags(const char *str) { function list_tags (line 3276) | static void list_tags(void) { function run (line 3291) | int run(int argc, char *argv[]) { FILE: gtc2vcf.h function heof (line 47) | static inline int heof(hFILE *hfile) { function read_bytes (line 54) | static inline void read_bytes(hFILE *hfile, void *buffer, size_t nbytes) { type dirent (line 70) | struct dirent function FILE (line 94) | static inline FILE *get_file_handle(const char *str) { function flank2fasta (line 106) | static inline void flank2fasta(const char *name, const char *flank, FILE... function bcf_hdr_name2id_flexible (line 128) | static inline int bcf_hdr_name2id_flexible(const bcf_hdr_t *hdr, char *c... function rev_nt (line 155) | static inline char rev_nt(char iupac) { function mask_nt (line 169) | static inline char mask_nt(char iupac) { function flank_reverse_complement (line 180) | static inline void flank_reverse_complement(char *flank) { function flank_left_shift (line 205) | static inline int flank_left_shift(char *flank) { function get_position (line 240) | static inline int get_position(htsFile *hts, sam_hdr_t *sam_hdr, bam1_t ... function strupper (line 345) | static inline void strupper(char *str) { function get_gc_ratio (line 353) | static inline float get_gc_ratio(const char *beg, const char *end) { function len_common_suffix (line 364) | static inline int len_common_suffix(const char *s1, const char *s2, size... function len_common_prefix (line 374) | static inline int len_common_prefix(const char *s1, const char *s2, size... function get_indel_alleles (line 388) | static inline int get_indel_alleles(kstring_t *allele_a, kstring_t *alle... function get_allele_b_idx (line 417) | static inline int get_allele_b_idx(char ref_base, char *allele_a, char *... function get_allele_a_idx (line 437) | static inline int get_allele_a_idx(int allele_b_idx) { function alleles_ab_to_vcf (line 450) | static inline int alleles_ab_to_vcf(const char **alleles, const char *re... function get_strand_from_top_alleles (line 478) | static inline int get_strand_from_top_alleles(char *allele_a, char *alle... function get_baf_lrr (line 524) | static inline void get_baf_lrr(float ilmn_theta, float ilmn_r, float aa_... FILE: idat2gtc.c function KSORT_INIT_GENERIC (line 248) | KSORT_INIT_GENERIC(float) function md5_hgetc (line 327) | static inline int md5_hgetc(hFILE *fp, hts_md5_context *md5) { function read_bytes (line 334) | static void read_bytes(hFILE *hfile, void *buffer, size_t nbytes, hts_md... function heof (line 347) | static int heof(hFILE *hfile) { function read_array (line 354) | static void read_array(hFILE *hfile, void **arr, size_t *m_arr, size_t n... function read_pfx_string (line 378) | static void read_pfx_string(hFILE *hfile, char **str, size_t *m_str, hts... function is_gzip (line 396) | static int is_gzip(hFILE *hfile) { function hwrite_uint16 (line 402) | static inline int hwrite_uint16(hFILE *hfile, uint16_t num) { return hwr... function hwrite_int32 (line 404) | static inline int hwrite_int32(hFILE *hfile, int32_t num) { return hwrit... function hwrite_pfx_string (line 407) | static int hwrite_pfx_string(hFILE *hfile, const char *str) { type chip_type_t (line 460) | typedef struct { type RunInfo (line 557) | typedef struct { type idat_t (line 565) | typedef struct { function idat_read (line 602) | static int idat_read(idat_t *idat, uint16_t id) { function idat_t (line 700) | static idat_t *idat_init(const char *fn, int load_arrays) { function idat_destroy (line 754) | static void idat_destroy(idat_t *idat) { function idat_to_csv (line 788) | static void idat_to_csv(const idat_t *idat, FILE *stream, int verbose) { function idats_to_tsv (line 830) | static void idats_to_tsv(idat_t **idats, int n, FILE *stream) { type XForm (line 902) | typedef struct { type ScannerData (line 920) | typedef struct { type SampleData (line 928) | typedef struct { type gtc_t (line 937) | typedef struct { function leb128_strlen (line 993) | static int leb128_strlen(const char *s) { function gtc_write (line 1001) | static int gtc_write(const gtc_t *gtc, const char *fn, int gtc_file_vers... function gtc_destroy (line 1154) | static void gtc_destroy(gtc_t *gtc) { type LocusEntry (line 1197) | typedef struct { function get_assay_type (line 1242) | static uint8_t get_assay_type(const char *allele_a_probe_seq, const char... function locusentry_read (line 1274) | static void locusentry_read(LocusEntry *locus_entry, hFILE *hfile, hts_m... type bpm_t (line 1337) | typedef struct { function bpm_t (line 1373) | static bpm_t *bpm_init(const char *fn, int eof_check, int make_dict, int... function bpm_destroy (line 1455) | static void bpm_destroy(bpm_t *bpm) { type ClusterStats (line 1505) | typedef struct { type ClusterScore (line 1513) | typedef struct { type ClusterRecord (line 1520) | typedef struct { type egt_t (line 1530) | typedef struct { function clusterscore_read (line 1550) | static void clusterscore_read(ClusterScore *clusterscore, hFILE *hfile, ... function clusterrecord_read (line 1557) | static void clusterrecord_read(ClusterRecord *clusterrecord, hFILE *hfil... function egt_t (line 1582) | static egt_t *egt_init(const char *fn, int eof_check, int checksum) { function egt_destroy (line 1672) | static void egt_destroy(egt_t *egt) { function sqr (line 1746) | inline static double sqr(double x) { return x * x; } function sqrf (line 1748) | inline static float sqrf(float x) { return x * x; } function matlab_linsolve0 (line 1752) | static int matlab_linsolve0(int n, const float *x, const float *y, doubl... function matlab_linsolve1 (line 1767) | static int matlab_linsolve1(int n, const float *x, const float *y, doubl... function matlab_wfit0 (line 1788) | static int matlab_wfit0(int n, const float *y, const float *x, const dou... function matlab_wfit1 (line 1803) | static int matlab_wfit1(int n, const float *y, const float *x, const dou... function matlab_nanmean (line 1825) | static float matlab_nanmean(int n, const float *vals) { function matlab_mean (line 1839) | static float matlab_mean(int n, const float *vals) { function matlab_median (line 1849) | static float matlab_median(int n, float *vals) { function matlab_madsigma_new (line 1861) | static double matlab_madsigma_new(int n, const double *r, int p) { function matlab_madsigma_old (line 1885) | static double matlab_madsigma_old(int n, const double *r, int p) { function matlab_robustfit0 (line 1906) | static void matlab_robustfit0(int n, const float *x, const float *y, dou... function matlab_robustfit1 (line 1947) | static void matlab_robustfit1(int n, const float *x, const float *y, dou... function findClosestSitesToPointsAlongAxis (line 2018) | int findClosestSitesToPointsAlongAxis(int n_raw, float *raw_x, float *ra... function percentile (line 2206) | static float percentile(int n, const float *vals, int percentile) { function matlab_iqr (line 2229) | static float matlab_iqr(int n, const float *vals) { function matlab_trimmean (line 2240) | static float matlab_trimmean(int n, float *vals, int percent) { function matlab_unique (line 2265) | static int matlab_unique(int n, int *indices) { function matlab_min (line 2286) | static float matlab_min(int n, const float *vals) { function matlab_max (line 2297) | static float matlab_max(int n, const float *vals) { function remove_outliers (line 2365) | static void remove_outliers(int *n, float *x, float *y) { function remove_offset (line 2436) | static void remove_offset(int n, float *x, float *y, int *naa, int **iaa... function handle_rotation (line 2509) | static void handle_rotation(int n, float *x, float *y, int *naa, int **i... function handle_shear (line 2565) | static void handle_shear(int n, float *x, float *y, int *nbb, int **ibb,... function base_handle_scale (line 2606) | static void base_handle_scale(int n, float *x, float *y, int gentrain_ve... function handle_scale (line 2683) | static void handle_scale(int n, float *x, float *y, int gentrain_version... function get_nn12_rr12 (line 2730) | static void get_nn12_rr12(int n, const float *x, const float *y, float *... function normalize_single_bin (line 2766) | static void normalize_single_bin(int n, float *x, float *y, int gentrain... function mirror_data (line 2784) | static void mirror_data(int n, float *x, float *y) { function rect_to_polar (line 2807) | static void rect_to_polar(int n, float *x, float *y) { function normalize_single_bin_single_channel (line 2849) | static void normalize_single_bin_single_channel(int n, float *x, float *... function XForm (line 2890) | static XForm *normalize(int n, const uint16_t *xin, const uint16_t *yin,... function matlab_zmf (line 2947) | static float matlab_zmf(float x, float a, float b) { function matlab_smf (line 2956) | static float matlab_smf(float x, float a, float b) { function matlab_normpdf_vleft (line 2965) | static double matlab_normpdf_vleft(float x, float mu, float sigma) { function matlab_normpdf_vright (line 2972) | static double matlab_normpdf_vright(float x, float mu, float sigma) { function matlab_normpdf (line 2979) | static double matlab_normpdf(float x, float mu, float sigma) { function raw_x_y2norm_x_y (line 2990) | static inline void raw_x_y2norm_x_y(uint16_t raw_x, uint16_t raw_y, floa... function norm_x_y2ilmn_theta_r (line 3003) | static inline void norm_x_y2ilmn_theta_r(float norm_x, float norm_y, flo... function median3 (line 3018) | static inline float median3(float a, float b, float c) { return fmaxf(fm... function ClusterRecord (line 3022) | static ClusterRecord *gen_std_flair(const ClusterRecord *cluster_record) { function modilik (line 3077) | static void modilik(ClusterRecord *c, float t, float r, double *Laa, dou... function compute_score_call_prelim (line 3162) | static float compute_score_call_prelim(float r, float t, const ClusterRe... function matlab_gbellmf (line 3294) | static double matlab_gbellmf(double x, double a, double b, double c) { function gencall_score_map (line 3302) | static double gencall_score_map(double x) { return pow(x, 0.35) * matlab... function rev_allele (line 3304) | static inline char rev_allele(char allele) { function get_base_call (line 3315) | static void get_base_call(const char *snp, const char *ilmn_strand, uint... function make_calls (line 3337) | static void make_calls(gtc_t *gtc, const bpm_t *bpm, const egt_t *egt, f... type gender_t (line 3402) | typedef struct { function estimate_gender (line 3416) | static void estimate_gender(gtc_t *gtc, const bpm_t *bpm, const egt_t *e... function get_baf_lrr (line 3489) | static inline void get_baf_lrr(float ilmn_theta, float ilmn_r, float aa_... function calculate_baf_lrr (line 3511) | static void calculate_baf_lrr(gtc_t *gtc, const bpm_t *bpm, const egt_t ... function calculate_intensity_percentiles (line 3552) | static void calculate_intensity_percentiles(gtc_t *gtc) { function compute_sample_stats (line 3592) | static void compute_sample_stats(gtc_t *gtc, const bpm_t *bpm, float gen... function get_int32_parameter (line 3674) | static int32_t get_int32_parameter(const char *str, const char *id) { function load_sample_section (line 3688) | static void load_sample_section(gtc_t *gtc, const idat_t *idat, int imag... function get32_index (line 3703) | static int32_t get32_index(void *dict, int32_t key) { function fill_array (line 3711) | static void fill_array(const idat_t *grn_idat, const idat_t *red_idat, c... function fill_controls_array (line 3747) | static void fill_controls_array(const idat_t *grn_idat, const idat_t *re... function gtc_t (line 3766) | static gtc_t *gtc_init(const idat_t *grn_idat, const idat_t *red_idat, c... function FILE (line 3921) | static inline FILE *get_file_handle(const char *str) { function round_adjust (line 3937) | static double round_adjust(double x) { function snp_map_write (line 3960) | static void snp_map_write(const bpm_t *bpm, const egt_t *egt, const char... function run (line 3985) | int run(int argc, char *argv[]) { FILE: nearest_neighbor.c function findClosestSitesToPointsAlongAxis (line 34) | int findClosestSitesToPointsAlongAxis(int n_raw, float *raw_x, float *ra...