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bwtool.h
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bwtool.h
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#ifndef BWTOOL_H
#define BWTOOL_H
#ifndef FLOAT_H
#include <float.h>
#endif
enum bw_op_type
{
invalid = 0,
not_equal = 1,
equal = 2,
less = 3,
less_equal = 4,
more = 5,
more_equal = 6,
mask = 7,
};
enum bw_op_type get_bw_op_type(char *thresh_type, boolean inverse);
/* speed things up inside loop. we don't want a string comparison for every datapoint */
/* to know what kind of operation to perform. */
void usage_remove();
/* Explain removal usage and exit. */
void usage_fill();
/* Explain fill usage and exit. */
void usage_shift();
/* Explain usage and exit. */
void usage_find();
/* Explain find usage and exit. */
void usage_distrib();
/* Explain usage of distribution program and exit. */
void usage_chromgraph();
/* Explain usage of chromgraph program and exit. */
void usage_distance();
/* Explain usage of distance calculation program and exit. */
void usage_aggregate();
/* Explain usage of aggregate program and exit. */
void usage_random();
/* Explain usage of randomized data program and exit. */
void usage_summary();
/* Explain usage of the summarize program and exit. */
void usage_matrix();
/* Explain usage of the matrix-creation program and exit. */
void usage_roll();
/* Explain the usage of the rolling-mean program and exit. */
void usage_sax();
/* Explain usage of the sax program and exit. */
void usage_split();
/* Explain usage of the splitting program and exit. */
void usage_lift();
/* Explain usage of the lift program */
void usage_paste();
/* Explain usage of paste program and exit. */
void usage_window();
/* Explain usage of the window-tiling program and exit */
void usage_extract();
/* Explain usage and exit. */
void bwtool_remove(struct hash *options, char *favorites, char *regions, unsigned decimals, enum wigOutType wot,
boolean condense, boolean wig_only, char *thresh_type, char *val_or_file, char *bigfile, char *tmp_dir,
char *outputfile);
/* bwtool_remove - main for removal program */
void bwtool_fill(struct hash *options, char *favorites, char *regions, unsigned decimals, enum wigOutType wot,
boolean condense, char *val_s, char *bigfile, char *tmp_dir, char *outputfile);
/* bwtool_fill - main for filling program */
void bwtool_find_extrema(struct hash *options, char *favorites, char *regions, unsigned decimals,
double fill, char *bigfile, char *tmp_dir, char *outputfile);
/* find local extrema */
void bwtool_find_thresh(struct hash *options, char *favorites, char *regions, double fill,
char *thresh_type, char *thresh_s, char *bigfile, char *tmp_dir, char *outputfile);
/* find regions fitting a specified threshold */
void bwtool_find_max(struct hash *options, char *favorites, char *regions, double fill,
char *bigfile, char *tmp_dir, char *outputfile);
/* find max points in a range */
void bwtool_distrib(struct hash *options, char *favorites, char *regions, unsigned decimals,
char *bigfile, char *tmp_dir, char *outputfile);
/* make plotting information about the bigWig's distribution */
void bwtool_chromgraph(struct hash *options, char *favorites, char *regions, unsigned decimals,
double fill, char *bigfile, char *tmp_dir, char *outputfile);
/* bwtool_chromgraph - main for making the chromgraph file */
void bwtool_aggregate(struct hash *options, char *regions, unsigned decimals, double fill,
char *size_s, char *region_list_s, char *wig, char *tmp_dir, char *output_file);
/* aggregate - main */
void bwtool_random(struct hash *options, char *favorites, char *regions, unsigned decimals,
double fill, char *num_s, char *size_s, char *bigfile, char *tmp_dir, char *output_file);
/* random - main */
void bwtool_summary(struct hash *options, char *favorites, char *regions, unsigned decimals,
double fill, char *loci_s, char *bigfile, char *tmp_dir, char *outputfile);
/* bwtool_summary - main for the summarize program */
void bwtool_shift(struct hash *options, char *favorites, char *regions, unsigned decimals, enum wigOutType wot,
boolean condense, char *val_s, char *bigfile, char *tmp_dir, char *outputfile);
/* bwtool_shift - main for shifting program */
void bwtool_split(struct hash *options, char *regions, char *size_s, char *bigfile, char *tmp_dir, char *outputfile);
/* bwtool_split - main for the splitting program */
void bwtool_matrix(struct hash *options, char *favorites, char *regions, unsigned decimals,
double fill, char *range_s, char *bigfile, char *tmp_dir, char *outputfile);
/* bwtool_matrix - main for matrix-creation program */
void bwtool_autocorr(struct hash *options, char *favorites, char *regions, unsigned decimals,
double fill, char *bigfile, char *tmp_dir, char *outputfile);
/* bwtool_autocorr - main for autocorrelation program */
void bwtool_sax(struct hash *options, char *favorites, char *regions, unsigned decimals,
char *alpha_s, char *bigfile, char *tmp_dir, char *outputfile);
/* bwtool_sax - main for the sax symbol program */
void bwtool_lift(struct hash *options, char *favorites, char *regions, unsigned decimals,
enum wigOutType wot, char *bigfile, char *tmp_dir, char *chainfile, char *outputfile);
/* bwtool_lift - main for lifting program */
void bwtool_paste(struct hash *options, char *favorites, char *regions, unsigned decimals, double fill,
enum wigOutType wot, struct slName **p_files, char *tmp_dir, char *output_file);
/* bwtool_paste - main for paste program */
void bwtool_window(struct hash *options, char *favorites, char *regions, unsigned decimals, double fill,
char *size_s, char *bigfile, char *tmp_dir, char *outputfile);
/* bwtool_window - main for the windowing program */
void bwtool_extract(struct hash *options, char *regions, unsigned decimals, double fill,
char *style, char *bigfile, char *tmp_dir, char *output_file);
/* bwtool_extract - main for the extract program */
void bwtool_roll(struct hash *options, char *favorites, char *regions, unsigned decimals, double fill,
enum wigOutType wot, char *command, char *size_s, char *bigfile, char *tmp_dir, char *outputfile);
/* bwtool_roll - main for the rolling-mean program */
#endif /* BWTOOL_H */