filter.h

/*  filter.h -- filter expressions.

    Copyright (C) 2013-2024 Genome Research Ltd.

    Author: Petr Danecek <pd3@sanger.ac.uk>

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of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
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The above copyright notice and this permission notice shall be included in
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.  */

#ifndef __FILTER_H__
#define __FILTER_H__

#include <htslib/vcf.h>

typedef struct _filter_t filter_t;

/**
  *  @hdr:  BCF header file
  *  @str:  see the bcftools filter command help for description.
  *         See also the extended usage described in filter_test_ext(),
  *         intended for programmatic access
  *  Same as filter_parse() but exits on errors
  */
filter_t *filter_init(bcf_hdr_t *hdr, const char *str);

void filter_destroy(filter_t *filter);

/**
  *  filter_test() - test whether the BCF record passes the test
  *  @samples:  if not NULL, a pointer to an array with samples statuses is
  *             stored in the location referenced by @samples. The pointer
  *             will be set to NULL if the FORMAT fields were not queried.
  *  Returns 1 if the expression is true and 0 if false.
  */
int filter_test(filter_t *filter, bcf1_t *rec, const uint8_t **samples);

/**
  *  filter_test_ext() - same as filter_test(), but sets some of the terms
  *        on the fly. An expression initialized with, say,
  *        "STR_TAG={} | INT_TAG={} | FLT_TAG={}" takes three
  *        additional pointer arguments which are expected to point to memory
  *        area occupied by the appropriate type, see also filter_ext_types().
  *        The type determination is not fool-proof, in such case the type can
  *        be given explicitly as eg "TAG={str}".
  *  @ext: array of size 'n_ext' occupied with pointers to the data types
  *        inferred from the expression given at the time of initialization.
  *        The pointers set to NULL will be treated as if missing value "."
  *        was given.
  *  @n_ext: the size of 'ext' array
  */
int filter_test_ext(filter_t *filter, bcf1_t *rec, const uint8_t **samples, const void **ext);

/**
  *  filter_set_samples() - restrict filtering expression to samples.
  *             Call after filter_init().
  *  @samples:  use samples set to 1, ignore samples set 0
  */
void filter_set_samples(filter_t *filter, const uint8_t *samples);

/**
  *  filter_get_doubles() - return a pointer to values from the last filter_test() evaluation
  */
const double *filter_get_doubles(filter_t *filter, int *nval, int *nval1);

int filter_max_unpack(filter_t *filter);

/**
  *  filter_ext_types() - returns the number and BCF_HT_* types of external values
  *         found in the filtering expression
  */
const int *filter_ext_types(filter_t *filter, int *n_ext);

/**
  *  Same as filter_init() but may not exit on some type of errors. The caller
  *  must check if the returned value is not NULL and if the consequent call
  *  of filter_status() returns FILTER_OK before the filter_pass() can be called.
  */
filter_t *filter_parse(bcf_hdr_t *hdr, const char *str);

#define FILTER_OK 0
#define FILTER_ERR_UNKN_TAGS 1
#define FILTER_ERR_OTHER 2

/**
  *  Check if filter_parse() was successful
  */
int filter_status(filter_t *filter);
const char **filter_list_undef_tags(filter_t *filter, int *nundef);
const char **filter_list_used_tags(filter_t *filter, int *nused);

#endif